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PubMed2005

A method to estimate the uncertainty of measurements in a conglomerate of instruments/laboratories.

A comparison of the performance, at two concentrations, of the measurement procedures for 23 common components is presented. For each component the within-, pure between- and total variations have been calculated and an imprecision profile indicated. Thus a pragmatic, readily and generally applicable method is advised to describe the performance of laboratories under repeatability and reproducibility conditions. The calculated total variation is compared with the results estimated from the biological variation of the properties. In most cases the within-laboratory variation is better than that given by the reference database, whereas in about half of the procedures the total variation exceeds that of the reference database. The outcome illustrates the transferability problems that multicentre studies and the diagnosis of patients face by measuring samples using a conglomerate of instruments/laboratories that are not aligned. The calculation procedures are detailed in an appendix and the calculation and presentation of the results are made with a custom-made worksheet program.

Clinical Laboratory Techniques↗

PubMed2005

Bone assessment in children: comparison of fan-beam DXA analysis.

The newest version of whole body dual-energy X-ray absorptiometry (DXA) analysis software from Hologic (Discovery 12.1) is designed to enhance bone detection in smaller subjects. We re-analyzed 1127 pediatric scans (ages 1.8-18.5 yr) previously analyzed using software version 11.2. Regression analysis compared new and original results for bone area (BA), bone mineral content (BMC), bone mineral density (BMD), and DXA-derived body weight. Changes in total and regional bone results were compared with age, weight, and height. New results were highly correlated with original analyses (R2 > or = 0.9), but there were large differences at the individual subject level. The BA and BMC values increased in subjects less than 40 kg weight, resulting in a lower BMD. Original and new results were equivalent by about age 14 yr in both genders. Regional bone data showed the greatest changes in the legs. The newest software produces significant changes in bone values in subjects weighing less than 40 kg, compared with earlier versions. This effect increases with decreasing body weight. This will impact interpretation of longitudinal pediatric DXA studies, as well as existing pediatric whole body bone reference databases. Investigators must recognize which DXAsoftware version they are using, and which version produced any reference database they may use for comparison.

Absorptiometry, Photon↗

PubMed2002

Social benefits of non-criminal genetic databases: missing persons and human remains identification.

A Missing Persons Genetic Identification Program (Phoenix Program) was implemented in Spain in order to try to identify cadavers and human remains that could not be identified using traditional forensic approaches; to our knowledge, this is the first database ever implemented and in function in the world. Two separate mitochondrial DNA (mtDNA) databases have been generated and comparisons can be made automatically to match identical or similar sequences contained in both databases. One database is called the Reference Database (RD), which contains mtDNA sequences from maternal relatives of missing persons that provide the samples voluntarily after informed consent. The other database is called the Questioned Database (QD) and is comprised of mtDNA data on unknown remains and cadavers that could not be unequivocally identified. The combined database is a civil database designed solely for human identification and because of the informed consent and voluntary donation of reference samples is different from other databases now used to solve criminal cases. It is timely and incumbent on other willing countries to begin an international collaboration so compatibility and full utility can be enjoyed with this kind of non-criminal database.

Cadaver↗

PubMed2003

Long-term ST database: a reference for the development and evaluation of automated ischaemia detectors and for the study of the dynamics of myocardial ischaemia.

The long-term ST database is the result of a multinational research effort. The goal was to develop a challenging and realistic research resource for development and evaluation of automated systems to detect transient ST segment changes in electrocardiograms and for supporting basic research into the mechanisms and dynamics of transient myocardial ischaemia. Twenty-four hour ambulatory ECG records were selected from routine clinical practice settings in the USA and Europe, between 1994 and 2000, on the basis of occurrence of ischaemic and non-ischaemic ST segment changes. Human expert annotators used newly developed annotation protocols and a specially developed interactive graphic editor tool (SEMIA) that supported paperless editing of annotations and facilitated international co-operation via the Internet. The database contains 86 two- and three-channel 24 h annotated ambulatory records from 80 patients and is stored on DVD-ROMs. The database annotation files contain ST segment annotations of transient ischaemic (1155) and heart-rate related ST episodes and annotations of non-ischaemic ST segment events related to postural changes and conduction abnormalities. The database is intended to complement the European Society of Cardiology ST-T database and the MIT-BIH and AHA arrhythmia databases. It provides a comprehensive representation of 'real-world' data, with numerous examples of transient ischaemic and non-ischaemic ST segment changes, arrhythmias, conduction abnormalities, axis shifts, noise and artifacts.

Adult↗

PubMed2002

Computational Analysis of Gene Identification with SAGE.

SAGE is one of the few techniques capable of uniformly probing gene expression at a genome level irrespective of mRNA abundance and without a priori knowledge of the transcripts present. However, individual SAGE tags can match many sequences in the reference database, complicating gene identification. We perform a baseline evaluation of gene identification with SAGE using UniGene Human as the reference database by analyzing 1) the distributions of tags for various length tag sets formed for UniGene Human and 2) the tag-to-sequence mapping using a SAGE tag set consisting of 37,522 tags derived from human myeloid cells. The extensive multiplicity of the dbEST component of UniGene significantly detracts from gains that might be expected by extending tags within the scope of the SAGE protocol. In order to achieve reasonable sequence specificity for gene identification with the content of the commonly used UniGene sequence collection, tags on the order of hundreds of bases in length are required. One way to produce tags of such lengths is with GLGI, which extends SAGE tags to the 3' end of cDNA. We show that the longer sequences produced by GLGI relieve significantly the multiple match condition. In the myeloid sample, we also found a correlation between multiple match severity and high copy number. We extrapolate these findings, providing insights into the use of UniGene Human as a reference for gene identification.

Animals↗

PubMed1994

Evaluation of Hinf I-generated VNTR profile frequencies determined using various ethnic databases.

Concerns have been raised about hypothetical problems arising from the use of statistics for determining the likelihood of occurrence of DNA profiles for forensic purposes. A major contention is that reference databases based on subgroups of a major population category rather than on general (or major) population groups, might yield large differences in the estimated likelihood of occurrence of DNA profiles. This hypothetical issue is based on the assertion by some people that the differences among subgroups within a race would be greater than between races (at least for forensic purposes). To evaluate the effects of the above concern the likelihood of occurrence of 615 Hinf I-generated target DNA profiles was estimated using fixed bin frequencies from various ethnic databases and the multiplication rule. Based on the data in this study, differences in allele frequencies at a particular locus do not have substantial effects on VNTR profile frequency estimates when subgroup reference databases from within a major population group are compared. In contrast, the greatest variation in statistical estimates occurs across-major population groups. Therefore, the assertion, by some critics that the differences among subgroups within a race would be greater than between races (at least for forensic purposes), is unfounded. The data in the study support that comparisons across major population groups provide valid estimates of DNA profile frequencies without forensically significant consequences. The data do not support the need for alternate procedures, such as the ceiling principle approach, for deriving statistical estimates of DNA profile frequencies.

Black People↗

PubMed2006

Computerized craniofacial reconstruction using CT-derived implicit surface representations.

In forensic craniofacial reconstruction, facial features of an unknown individual are estimated from an unidentified skull, based on a mixture of experimentally obtained guidelines on the relationship between soft tissues and the underlying skeleton. In this paper, we investigate the possibility of using full 3D cross-sectional CT images for establishing a reference database of densely sampled distances between the external surfaces of the skull and head for automated craniofacial reconstruction. For each CT image in the reference database, the hard tissue (skull) and soft tissue (head) volumes are automatically segmented and transformed into signed distance transform (sDT) images, representing for each voxel in this image the Euclidean distance to the closest point on the skull and head surface, respectively, distances being positive (negative) for voxels inside (outside) the skull/head. Multiple craniofacial reconstructions are obtained by first warping each reference skull sDT maps to the target skull sDT using a B-spline based free form deformation algorithm and subsequently applying these warps to the reference head sDT maps. A single reconstruction of the target head surface is defined as the zero level set of the arithmetic average of all warped reference head sDT maps, but other reconstructions are possible, biasing the result to subject specific attributes (age, BMI, gender). Both qualitative and quantitative tests (measuring the similarity between the 3D reconstructed and corresponding original head surface) on a small (N = 20) database are presented to proof the validity of the concept.

Databases as Topic↗

PubMed2005

Spectral magnitude effects on the analyses of secondary structure from circular dichroism spectroscopic data.

The effects of spectral magnitude on the calculated secondary structures derived from circular dichroism (CD) spectra were examined for a number of the most commonly used algorithms and reference databases. Proteins with different secondary structures, ranging from mostly helical to mostly beta-sheet, but which were not components of existing reference databases, were used as test systems. These proteins had known crystal structures, so it was possible to ascertain the effects of magnitude on both the accuracy of determining the secondary structure and the goodness-of-fit of the calculated structures to the experimental data. It was found that most algorithms are highly sensitive to spectral magnitude, and that the goodness-of-fit parameter may be a useful tool in assessing the correct scaling of the data. This means that parameters that affect magnitude, including calibration of the instrument, the spectral cell pathlength, and the protein concentration, must be accurately determined to obtain correct secondary structural analyses of proteins from CD data using empirical methods.

Albumins↗

PubMed2026

Effectiveness of mass spectrometry and genomic analysis in the surveillance of nontuberculous Mycobacterium in Taiwan.

Nontuberculous mycobacteria (NTM) are diverse, and species-level identification remains challenging in routine diagnostics. We analyzed NTM isolates collected at three regional centers of the National Taiwan University Hospital (NTUH) from 2019 to 2024 to assess geographic variation and identification performance after implementation of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Among 3,188 cases meeting the microbiological criteria for probable pulmonary NTM disease, the species distribution differed by region: Mycobacterium avium complex predominated in central Taiwan (Yunlin, 47.3%), whereas M. abscessus complex (Taipei, 26.5%) and M. kansasii (Hsinchu, 12.4%) were more common in northern Taiwan. In 2019, 14.5% of isolates were reported to be unidentified by MALDI-TOF MS; with workflow optimization and database updates, this percentage decreased but plateaued at 4.5-4.8%. Whole-genome sequencing (WGS) of 61 randomly selected persistently unidentified isolates revealed eight average nucleotide identity (ANI)-defined clusters; 55 isolates (90.2%) could not be assigned to known species using current reference databases. Two clusters detected only in Hsinchu were phylogenetically closest to M. kyorinense, with ANI values below the species demarcation threshold. Overall, we observed marked regional heterogeneity of NTM in Taiwan and a persistent identification gap that remained after MALDI-TOF MS optimization and follow-up WGS.IMPORTANCEThis study characterized regional differences in the NTM species distribution across Taiwan, and the results highlight the limitations of current identification approaches. MALDI-TOF MS identifies most isolates, but locally circulating lineages represent a persistent gap in global reference libraries. Even with whole-genome sequencing (WGS), 90.2% (55/61) of persistently unresolved isolates could not be assigned to known species in the current reference databases despite the formation of clear ANI- and phylogeny-defined clusters. These findings show that both proteomic and genomic reference resources for clinical NTM remain incomplete. Expanding regionally representative databases and performing WGS for isolates that remain unresolved by MALDI-TOF MS will be necessary to improve species-level resolution for surveillance and clinical interpretation.

Taiwan↗

PubMed1999

High cost factors for leukaemia and lymphoma patients: a new analysis of costs within these diagnosis related groups.

STUDY OBJECTIVE: To determine high cost factors to help managers and clinicians to analyse the reasons of adverse costs and provide indications for financial negotiation. DESIGN: To locate high cost or long stay patients, the analysis was designed on the basis of a mixture of Weibull distributions. In this new model, the proportion of high cost patients was expressed according to the multinomial logistic regression, permitting the determination of high cost factors. SETTING: The 1993 French reference database, constituted in the framework of the national study of DRG costs, conducted by the French Ministry of Health. The database of discharge abstracts recorded in 1993 in the Dijon public teaching hospital. PARTICIPANTS: The analyses were based on 1352 abstracts from the French reference database and 368 from the Dijon database concerning patients, aged 18 and over, suffering from leukaemia and lymphoma. MAIN RESULTS: High cost and long stay factors were the same: number of stays, death, transfer, acute leukaemia, neutropenia, septicaemia, high dose aplastic chemotherapy, central venous catheterisation, parenteral nutrition, protected or laminar airflow room, blood transfusion, and intravenous antibiotherapy. CONCLUSIONS: Taking into account high cost predictive factors, as shown in the case of leukaemia and lymphoma patients, would help to reduce the adverse effects of a prospective payment system.

Adolescent↗

PubMed1992

Comparison of the effect of different reference data on Lunar DPX and Hologic QDR-1000 dual-energy X-ray absorptiometers.

We have investigated whether the Lunar DPX (software 3.4) and Hologic QDR-1000 dual-energy X-ray absorptiometers have comparable normal reference databases for the spine and femur of white UK and USA subjects. After conversion for systematic differences in absolute bone density values between the two systems, the reference databases were very similar for the spine in young subjects, but there were clear differences in the femur databases of young females and males of all ages. These differences were confirmed by comparing the percent age-matched and young values determined by the two systems for subjects scanned on both systems. Thus the diagnosis and management of a patient could differ, depending on the system used for the bone density measurements.

Absorptiometry, Photon↗

PubMed1999

Identification of patients to include in trauma audit: a modification of the pre-chart.

Trauma audit is commonly focused using a Pre-Chart to illustrate calculations made using the TRISS model. A line is drawn at Ps = 0.5 to divide expected survivors and nonsurvivors. The use of this cut-off in a severely injured population was examined. The 'M statistic' for a group of injured patients selectively triaged to a Trauma Centre was calculated. The ideal cut-off point between predicted outcomes when using the TRISS model to focus trauma audit in this population was determined using a Receiver Operating Characteristic (ROC) curve. For this population the TRISS 'M statistic' was 0.71 (indicating a significantly different case mix from the reference database) and the best cut-off point was at Ps = 0.76. Trauma audit in populations with a case mix of injury severity different from the reference database should use a different Ps line to define unexpected outcomes.

Humans↗

PubMed2004

The impact of SNPs on the interpretation of SAGE and MPSS experimental data.

Serial Analysis of Gene Expression (SAGE) and Massively Parallel Signature Sequencing (MPSS) are powerful techniques for gene expression analysis. A crucial step in analyzing SAGE and MPSS data is the assignment of experimentally obtained tags to a known transcript. However, tag to transcript assignment is not a straightforward process since alternative tags for a given transcript can also be experimentally obtained. Here, we have evaluated the impact of Single Nucleotide Polymorphisms (SNPs) on the generation of alternative SAGE and MPSS tags. This was achieved through the construction of a reference database of SNP-associated alternative tags, which has been integrated with SAGE Genie. A total of 2020 SNP-associated alternative tags were catalogued in our reference database and at least one SNP-associated alternative tag was observed for approximately 8.6% of all known human genes. A significant fraction (61.9%) of these alternative tags matched a list of experimentally obtained tags, validating their existence. In addition, the origin of four out of five SNP-associated alternative MPSS tags was experimentally confirmed through the use of the GLGI-MPSS protocol (Generation of Long cDNA fragments for Gene Identification). The availability of our SNP-associated alternative tag database will certainly improve the interpretation of SAGE and MPSS experiments.

DNA Restriction Enzymes↗

PubMed2002

North American male reference population for speed of sound in bone at multiple skeletal sites.

Alternatives to dual-energy X-ray absorptiometry (DXA) have been sought to increase access to low-cost osteoporosis risk assessment. Early quantitative ultrasound (QUS) systems measured speed of sound (SOS) and broadband ultrasound attenuation (BUA) at the calcaneus, and these were demonstrated to be good predictors of hip fracture risk. Recent studies have demonstrated the usefulness of other peripheral sites to assess bone status. The Sunlight Omnisense (Sunlight Medical, Rehovot, Israel) is a portable, inexpensive QUS device capable of multiple-site SOS measurement. To provide a robust male reference database, 588 healthy Caucasian males aged 20-90 yr were recruited from 6 centers across North America. SOS measurements were taken at the distal 1/3 radius, proximal third phalanx, midshaft tibia, and fifth metatarsal. A female reference database has previously been collected at North American sites. The results indicate that SOS in males exhibits an age-related decline beginning in the fifth decade at the radius, phalanx, and metatarsal, whereas the tibial SOS remains nearly constant until the ninth decade. Although females reach a higher-peak SOS than males at most sites, SOS is higher in males at all sites after the sixth decade, as a result of a more gradual decline in SOS. Longitudinal monitoring of healthy men should be performed to confirm these cross-sectional results.

Adult↗

PubMed1997

Comparison of Hae-III-generated VNTR profiles of Chinese in Hong Kong and Singapore.

Some statistical analysis and experiments have been carried out on the single-locus VNTR reference databases collected separately from the Chinese in Hong Kong and Singapore to assess the issues of sample size and representativeness in the context of forensic science. We employed the bootstrap method and the Pearson chi-squared test for independence, and found that the different reference databases have very little effect in assessing the frequencies of occurrence of variable number of tandem repeats (VNTR) profiles. The results of random match probability assessment also indicate that the sample sizes studied appeared adequate to provide representative data. It has been found that a battery of four loci was enough to distinguish the 458 individuals under study.

Asian People↗

PubMedDate not supplied

An ontology for pharmaceutical ligands and its application for in silico screening and library design.

Annotation efforts in biosciences have focused in past years mainly on the annotation of genomic sequences. Only very limited effort has been put into annotation schemes for pharmaceutical ligands. Here we propose annotation schemes for the ligands of four major target classes, enzymes, G protein-coupled receptors (GPCRs), nuclear receptors (NRs), and ligand-gated ion channels (LGICs), and outline their usage for in silico screening and combinatorial library design. The proposed schemes cover ligand functionality and hierarchical levels of target classification. The classification schemes are based on those established by the EC, GPCRDB, NuclearDB, and LGICDB. The ligands of the MDL Drug Data Report (MDDR) database serve as a reference data set of known pharmacologically active compounds. All ligands were annotated according to the schemes when attribution was possible based on the activity classification provided by the reference database. The purpose of the ligand-target classification schemes is to allow annotation-based searching of the ligand database. In addition, the biological sequence information of the target is directly linkable to the ligand, hereby allowing sequence similarity-based identification of ligands of next homologous receptors. Ligands of specified levels can easily be retrieved to serve as comprehensive reference sets for cheminformatics-based similarity searches and for design of target class focused compound libraries. Retrospective in silico screening experiments within the MDDR01.1 database, searching for structures binding to dopamine D2, all dopamine receptors and all amine-binding class A GPCRs using known dopamine D2 binding compounds as a reference set, have shown that such reference sets are in particular useful for the identification of ligands binding to receptors closely related to the reference system. The potential for ligand identification drops with increasing phylogenetic distance. The analysis of the focus of a tertiary amine based combinatorial library compared to known amine binding class A GPCRs, peptide binding class A GPCRs, and LGIC ligands constitutes a second application scenario which illustrates how the focus of a combinatorial library can be treated quantitatively. The provided annotation schemes, which bridge chem- and bioinformatics by linking ligands to sequences, are expected to be of key utility for further systematic chemogenomics exploration of previously well explored target families.

Combinatorial Chemistry Techniques↗

PubMed2004

Potential role of body surface ECG mapping for localization of atrial fibrillation trigger sites.

Catheter ablation has revolutionized the clinical management of atrial fibrillation (AF) by offering a curative treatment option for this highly prevalent arrhythmia. Ablation therapy is aimed at electrical isolation of the pulmonary veins (PVs) as a means to prevent rapidly firing focal activation within the PVs from penetrating into the left atrium (LA) and initiate reentrant wavelet propagation. However, non-PV AF trigger sites may be present and lead to unsuccessful ablation or post-ablation AF recurrences. Infrequent trigger firing and the difficulty or inability to induce focal trigger activity in the electrophysiology laboratory limits invasive catheter-based mapping of non-PV trigger sites. Identification of AF trigger sites using the surface electrocardiogram (ECG) P wave morphology is feasible but conventional 12-lead scalar recordings do not offer the resolving power to provide discrete regional localization to potentially target catheter ablation. The present paper includes a review of preliminary clinical data on the use of a 65-lead ECG mapping system (Resolution Medical, Inc) for the non-invasive localization of AF trigger sites. This method utilizes a unique previously developed reference database of 34 mean paced P wave integral map patterns which are each specific to activation arising from a discrete segment in the LA and right atrium (RA). Trigger site localization is obtained by matching the P wave integral map morphology of a premature atrial contraction (PAC) with the reference database of 34 mean paced P wave integral map patterns.

Algorithms↗

PubMed2001

Diagnostics of neisseriaceae and moraxellaceae by ribosomal DNA sequencing: ribosomal differentiation of medical microorganisms.

Fast and reliable identification of microbial isolates is a fundamental goal of clinical microbiology. However, in the case of some fastidious gram-negative bacterial species, classical phenotype identification based on either metabolic, enzymatic, or serological methods is difficult, time-consuming, and/or inadequate. 16S or 23S ribosomal DNA (rDNA) bacterial sequencing will most often result in accurate speciation of isolates. Therefore, the objective of this study was to find a hypervariable rDNA stretch, flanked by strongly conserved regions, which is suitable for molecular species identification of members of the Neisseriaceae and Moraxellaceae. The inter- and intrageneric relationships were investigated using comparative sequence analysis of PCR-amplified partial 16S and 23S rDNAs from a total of 94 strains. When compared to the type species of the genera Acinetobacter, Moraxella, and Neisseria, an average of 30 polymorphic positions was observed within the partial 16S rDNA investigated (corresponding to Escherichia coli positions 54 to 510) for each species and an average of 11 polymorphic positions was observed within the 202 nucleotides of the 23S rDNA gene (positions 1400 to 1600). Neisseria macacae and Neisseria mucosa subsp. mucosa (ATCC 19696) had identical 16S and 23S rDNA sequences. Species clusters were heterogeneous in both genes in the case of Acinetobacter lwoffii, Moraxella lacunata, and N. mucosa. Neisseria meningitidis isolates failed to cluster only in the 23S rDNA subset. Our data showed that the 16S rDNA region is more suitable than the partial 23S rDNA for the molecular diagnosis of Neisseriaceae and Moraxellaceae and that a reference database should include more than one strain of each species. All sequence chromatograms and taxonomic and disease-related information are available as part of our ribosomal differentiation of medical microorganisms (RIDOM) web-based service (http://www.ridom.hygiene.uni-wuerzburg.de/). Users can submit a sequence and conduct a similarity search against the RIDOM reference database for microbial identification purposes.

DNA, Ribosomal↗