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PubMed2003

Development of human protein reference database as an initial platform for approaching systems biology in humans.

Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization were extracted from the literature for a nonredundant set of 2750 human proteins. Almost all the information was obtained manually by biologists who read and interpreted >300,000 published articles during the annotation process. This database, which has an intuitive query interface allowing easy access to all the features of proteins, was built by using open source technologies and will be freely available at http://www.hprd.org to the academic community. This unified bioinformatics platform will be useful in cataloging and mining the large number of proteomic interactions and alterations that will be discovered in the postgenomic era.

BRCA1 Protein↗
PubMed2006

Normative reference database for bone mineral density in Indian men and women using digital X-ray radiogrammetry.

Osteoporosis is a major healthcare problem around the world and its importance lies in the fractures that result. A variety of devices are available in India and other Asian countries for bone mineral density (BMD) assessment, but their clinical utility is limited because of non-availability of local normative database. The purpose of this study was to establish the normative reference database for BMD in Indian women and men using digital x-ray radiogrammetry (DXR). Radiographs of the non-dominant hand were obtained on 262 women and 178 men between 20 and 79 years of age following strict inclusion and exclusion criteria. The radiographs were analysed by DXR using pronosco x-posure system V.2 to estimate the BMD (DXR-BMD). The peak value for DXR-BMD in women was 0.588 g/cm2 at age 35 years and 0.602 g/cm2 in men at age 42 years. There were statistically significant differences in BMD in women and men across all age ranges. An age dependent decline in BMD was seen in both women and men over the age of 50 years. The use of DXR should broaden the availability of fracture risk assessments in places where DXA is not available.

Absorptiometry, Photon↗
PubMed2002

Online Y-chromosomal short tandem repeat haplotype reference database (YHRD) for U.S. populations.

We describe here an online Y-chromosomal short tandem repeat haplotype reference database (YHRD) for U.S. populations, which represents 9-locus Y-STR haplotypes for 1705 African-Americans, European-Americans and Hispanics as of October 2001. This database is available online (http://www.ystr. org/usa/), free to access and was generated in order to supply the U.S. forensic DNA community with a valuable resource for frequencies of complete or incomplete 9-locus Y-STR haplotypes, as well as information about typing protocols and population genetic analyses. Pairwise R(ST)-statistics derived from the Y-STR haplotypes indicate no significant substructure among African-American populations from different regions of the U.S., nor (usually) among European-American and Hispanic populations. Thus, pooling of Y-STR haplotype data from regional populations within these three major groups is appropriate in order to obtain larger sample sizes. However, pooling of different major populations is generally not recommended due to statistically significant differences between African-American populations and all European-American/Hispanic populations, as well as between some European-American and Hispanic populations.

Black People↗
PubMed2005

Broadband ultrasound attention reference database for southeast Asian males and females.

INTRODUCTION: The objective of this study was to establish the broadband ultrasound attenuation (BUA) measurements of the calcaneum for Southeast Asian males and females. A database was used to draw the reference curve for the Southeast Asian male and female population. MATERIALS AND METHODS: The database included 366 healthy females and 236 healthy males. We measured the BUA values of the left heel using the Contact Ultrasound Bone Analyser (CUBA) clinical system. RESULTS: The mean difference between Southeast Asian males and Caucasian males was 9.3 dB MHz-1 and that for females was 5.0 dB MHz-1. The standard deviations (SDs) for Southeast Asian female and male normative values were 17.43 and 20.10, respectively. This is comparable with the SD for the McCue Caucasian female and male normative data of 16.54 and 17.45 respectively. CONCLUSION: The study shows that the Southeast Asian population has a significantly lower normative value than the Caucasian population. This BUA reference database obtained will allow for more accurate determination of Southeast Asian patients at risk of osteoporosis.

Adult↗
PubMed2000

Reference database for bone speed of sound measurement by a novel quantitative multi-site ultrasound device.

The nonuniform skeletal involvement in osteoporosis argues for multi-site evaluation. The Sunlight Omnisense (Sunlight Ultrasound Technologies, Israel) is a multi-site device that measures speed of sound (SOS) at the appendicular skeleton. We report the reference database for SOS at the radius (RAD), tibia (TIB), metatarsus (MTR) and phalanx (PLX). The database was obtained from 1521 healthy Israeli women (age 20-90 years) out of 2051 respondents. SOS was determined in 97.6% of the participants at the PLX, 96.4% at the TIB, 93.6% at the RAD and 85.1% at the MTR; it was not measurable in 0.5%. Short-term coefficient of variation was lowest at the RAD and always less than 1%. Maximal SOS was noted at 35-45 years of age in three of the sites (RAD 4169 m/s, MTR 3663 m/s, PLX 4047 m/s, respectively) but 10 years earlier at the TIB (3939 m/s). In the perimenopausal period (age 46-55 years), SOS was always lower in post- as compared with premenopausal women (p<0.05). Immediately following the menopause, SOS annually declined close to the short-term CV: 16, 34, 37 and 13 m/s at the RAD, PLX, MTR and TIB, respectively. The average age-stratified SOS values at various measurement sites were highly correlated at the population level (0.96-0.99), but less so at the individual level (0.40-0.57). Therefore, multi-site SOS measurements are better than single-site assessment. After 79 years of age, the average T-score at the RAD and PLX was <--2.5. This is similar to that of dual-energy X-ray absorptiometry (DXA)-determined spine bone mineral density (BMD) and somewhat lower than hip BMD. Equivalent T-score curves obtained by percentile adjustment of SOS at various sites to that of the RAD (at age group 60-69 years) reveal convergence and indicate that 52-68% of women older than 79 years are osteoporotic. In conclusion, multi-site peripheral SOS measurements reveal age-dependent bone changes with a high degree of measurement precision and indicate a prevalence of osteoporosis similar to that obtained by DXA.

Adult↗
PubMed2004

Human protein reference database as a discovery resource for proteomics.

The rapid pace at which genomic and proteomic data is being generated necessitates the development of tools and resources for managing data that allow integration of information from disparate sources. The Human Protein Reference Database (http://www.hprd.org) is a web-based resource based on open source technologies for protein information about several aspects of human proteins including protein-protein interactions, post-translational modifications, enzyme-substrate relationships and disease associations. This information was derived manually by a critical reading of the published literature by expert biologists and through bioinformatics analyses of the protein sequence. This database will assist in biomedical discoveries by serving as a resource of genomic and proteomic information and providing an integrated view of sequence, structure, function and protein networks in health and disease.

Computational Biology↗
PubMed2003

Reference database for dual X-ray and laser Calscan bone densitometer.

The new dual X-ray and laser technology (DXL) gives a more accurate determination of bone mineral density (BMD) than ordinary dual X-ray absorptiometry (DXA) technology because of the ability to eliminate fat tissue both inside and outside the measured bone. In this study the reference database for BMD measured at the calcaneus by the DXL Calscan device is reported. The database was obtained from 993 healthy women and 459 healthy men in a population from southern Sweden. Inclusion criteria were: healthy Swedish Caucasians, 15-85 yr of age for women and 19-85 yr of age for men, no history of osteoporosis treatment, no use of corticosteroids for more than 3 mo, and no extended bed rest. The young adult reference mean BMD for women was found to be 0.483 +/- 0.062 g/cm2 and for men 0.556 +/- 0.074 g/cm2. The age-adjusted odds ratio was 3.7 for a history of fracture among women aged 50 yr and over, comparing subjects with a 1-SD reduction in bone density to subjects with a bone density above this value. The DXL Calscan device used for the study was calibrated weekly against a heel bone phantom. The precision of these measurements was 0.5%. The in vivo precision was 1.2%, as assessed by duplicate measurements on 35 healthy individuals (mean age 52 yr, range 25-72 yr).

Absorptiometry, Photon↗
PubMed2006

Y chromosome haplotypes in Central-South Italy: implication for reference database.

One hundred and fifty individuals have been sampled across Central-South Italy and genotyped for Y chromosome STRs by PowerPlex Y system. Comparison with previous Italian databases revealed that majority of Y chromosome variation still need to be sampled. Identification of locus duplications, distribution of genetic variation and firstly identified alleles point to the necessity of more focused sampling strategies for reference databases.

Chromosomes, Human, Y↗
PubMed1997

The occurrence of false-positive technetium-99m sestamibi bull's eye defects in different reference databases. A study of an age- and gender-stratified healthy population.

Myocardial perfusion single-photon emission tomographic (SPET) imaging has been shown to be sensitive in the detection of coronary artery disease (CAD), whereas its specificity has been suboptimal. The aim of the present study was to study the frequency of abnormal bull's eye perfusion defects in a large age-stratified group of healthy subjects undergoing myocardial SPET assessed by comparison with two existing commercially available reference databases. One hundred and twenty-eight healthy volunteers (76 males and 52 females) with a less than 5% likelihood of CAD underwent rest and exercise technetium-99m sestamibi SPET. The false-positive response rate, defined as a significant reversible defect, was 12% when compared to the CEqual database and 29% when compared to the Cedars-Sinai database. With the CEqual program, rest defects occurred in 12% of the subjects. Defects occurred more often in women than in men, but the difference did not attain statistical significance. Significant defects were most frequent in the inferior wall and in women in the anterior wall as well. The distribution of defects was independent of age. Our results suggest that the specificity of 99mTc-sestamibi myocardial SPET using commercially available reference files is suboptimal. The risk of obtaining a false-positive test result in subjects undergoing 99mTc-sestamibi myocardial SPET with a very low likelihood of CAD was higher than anticipated. With both reference files false-positive test results were most frequently observed in the inferior wall. Our data suggest that commercial reference files for myocardial SPET need to be optimised, and should be used with caution. The use of attenuation correction may prove to be a major step forward.

Adult↗
PubMed2003

Patient assessment using standardized bone mineral density values and a national reference database: implementing uniform thresholds for the reimbursement of osteoporosis treatments in Belgium.

Dual-energy X-ray absorptiometry (DXA) devices from the three main manufacturers provide different bone mineral density (BMD) values, due in part to technical differences in the algorithms for bone mineral content (BMC) and area measurements and in part to the use of different manufacturer-derived reference databases. As a result, significant differences exist between Hologic, Lunar and Norland systems in the reported young normal standard deviation scores or T-scores. In a number of European countries, including Belgium, a T-score below -2.5 is one of the key criteria for reimbursement of osteoporosis treatments. This paper addresses the first attempt to implement a nationwide, uniform expression of BMD in patients, in order to harmonize drug reimbursement. To this end, measures were taken to implement a uniform expression of BMD in Belgian patients, by converting each manufacturer's absolute BMD to standardized BMD (sBMD) values and by establishing a single national reference range.

Absorptiometry, Photon↗
PubMed2003

Asian online Y-STR Haplotype Reference Database.

For several years Y-chromosomal microsatellites (short tandem repeats, STRs) have been well established in forensic practice. In this context, the genetic characteristics of the Y chromosome (i.e. its paternal inheritance and lack of recombination) render STRs particularly powerful. However, genetic differences between male populations appear to be larger for Y-STRs than for autosomal STRs, a fact that is most likely due to the higher sensitivity of Y-chromosomal lineages to genetic drift (Forensic Sci Int 118 (2001) 153). The assessment of probabilities for matches between haplotyped male persons or traces/persons requires the typing of a large number of haplotypes in the appropriate reference populations. The haplotype data of a large number of European as well as South and North American populations have been collected and are continuously published online (Y-STR Haplotype Reference Database--YHRD; http://www.ystr.org). The most recent multicentric effort has led to the establishment of an Asian YHRD (http://www.ystr.org/asia) which has been available since January 2002. All databases are maintained and curated at the Institute of Legal Medicine, Humboldt-University, Berlin and will soon be fused to a global repository including populations from all continents.

Asia↗
PubMed1992

Human liver protein map: a reference database established by microsequencing and gel comparison.

This publication establishes a reference human liver protein map obtained with immobilized pH gradients. By microsequencing, 57 spots or 42 polypeptide chains were identified. By protein map comparison and matching (liver, red blood cell and plasma sample maps), 8 additional proteins were identified. The new polypeptides and previously known proteins are listed in a table and/or labeled on the protein map, thus providing a human liver two-dimensional gel database. This reference map can be used to identify protein spots on other samples such as rectal cancer biopsies.

Amino Acid Sequence↗
PubMed2002

A reference database for tumor-related genes co-expressed with interleukin-8 using genome-scale in silico analysis.

BACKGROUND: The EST database provides a rich resource for gene discovery and in silico expression analysis. We report a novel computational approach to identify co-expressed genes using EST database, and its application to IL-8. RESULTS: IL-8 is represented in 53 dbEST cDNA libraries. We calculated the frequency of occurrence of all the genes represented in these cDNA libraries, and ranked the candidates based on a Z-score. Additional analysis suggests that most IL-8 related genes are differentially expressed between non-tumor and tumor tissues. To focus on IL-8's function in tumor tissues, we further analyzed and ranked the genes in 16 IL-8 related tumor libraries. CONCLUSIONS: This method generated a reference database for genes co-expressed with IL-8 and could facilitate further characterization of functional association among genes.

Journal Article↗
PubMed1999

Reference database of hypervariable genetic markers of Argentina: application for molecular anthropology and forensic casework.

The population of Argentina is mostly composed of people of European ancestry. Aboriginal communities are at present very reduced in number and restricted to small geographically isolated patches. Three aboriginal communities, the Mapuche, Tehuelche and Wichi, were selected for short tandem repeat (STR) investigation. The metropolitan population of the city of Buenos Aires was analyzed, with both micro- and minisatellites. The minisatellite loci D1S7, D2S44, D4S139, D5S110, D8S358, D10S28, and D17S26 were typed on HaeIII-digested DNA obtained from unrelated individuals. D1S80 was typed by polymerase chain reaction (PCR). The autosomal STRs THO1, FABP, D6S366, CSF1PO, TPOX, F13A1, FES/FPS, vWA, MBPA/B, D16S539, D7S820, D13S317, and RENA4 and the sex chromosome STRs HPRTB, DYS385, DYS3891, DYS38911, DYS19, DYS390, DYS391, DYS392, DYS393 and YCAII were also investigated. As a by-product of our investigations, a reference database was created that is routinely used in forensic casework and paternity testing. STR allele frequency distributions are characterized by significant differences within and also between different populations. In contrast, the minisatellite bin distribution of the metropolitan population is not significantly different from other Caucasian populations.

Alleles↗
PubMed2002

Multilingual approach to ICD10: on the need for a source reference database.

The distribution of ICD10 is of concern for thousand of developers in numerous countries. The absence of some basic features to facilitate the transfer and consequently to augment the quality of the delivered version is a constant characteristic. Errors, ambiguities, missing terms, unrecognised attributes are quite common, despite the efforts of some national centres doing their best to fill this gap. For other countries and languages, where such centres do not exist or do not have sufficient resources, this problem is even stronger. A reference ICD database is clearly a need today. The following features are to be made available out of an ICD database: exact count of terms, whether they are systematic, include, exclude or daggers and asterisks pairs, eventually at chapter level; exact count of notes, references and indirect exclusions; recommended structure of relational tables for ICD representation; basic structure of the classification at any level of detail. These features are somewhat language dependant and should be repeated for each one. This paper demonstrates the benefits of publishing such ICD reference information in order to improve the future ICD tools to be developed in numerous countries.

Database Management Systems↗