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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↗
PubMed1998

How the new Hologic hip normal reference values affect the densitometric diagnosis of osteoporosis.

In February 1997, Hologic supplied new software to all QDR dual-energy X-ray absorptiometry (DXA) machines replacing the previous femoral normative reference database with the NHANES III normative data. In addition to changing the normative database (and therefore T-scores) for all regions of the hip, the new software has changed the primary region of interest from the femoral neck to the total hip. In the present study we examined how these changes influence the densitometric diagnosis of osteoporosis in a large clinical referral population (n = 2311, mean age 62.7 years). The patients had spine and hip DXA performed at either of two centers using a Hologic QDR-2000 over a 4-year period. T-scores were derived for each patient using both previous and current young normal reference databases. Intraindividual differences in T-scores were calculated. The prevalence of osteoporosis based on the two normative databases and the difference between the prevalence was calculated for each skeletal site. The average paired difference between current and previous T-scores at femoral neck is 0.64, the difference increasing with age. Using the new normative database, the percentage of osteoporotic patients decreases from 49% of all patients at the femoral neck to 28% at the femoral neck and 20% at the total hip. In conclusion, the densitometric diagnosis of osteoporosis will be affected in a significant proportion of women as a result of the implementation of the new hip normative database supplied by Hologic. Whether this will translate into fewer patients being treated remains to be seen.

Absorptiometry, Photon↗
PubMed1997

Bone mineral density measurements using the Hologic QD2000 in 175 Singaporean women aged 20-80.

AIMS: The first aim is to obtain a reference database of bone mineral density (BMD) measurements for Singaporean women across different age groups and to compare this with an American database using the same machine. The second is to study the lifestyle factors that may influence bone mass in these women. METHODS: Subjects were recruited from hospital staff and their relatives. They needed to fulfil inclusion criteria and those with confounding factors such as being on hormone replacement therapy (HRT) were excluded. A lifestyle questionnaire was administered. RESULTS: Across every five-year age band, the mean BMD measurements of the Singaporean women were 3%-8% lower than their American counterparts at the AP spine and 6%-11% lower at the femoral neck. 40.6% either drank milk, ate cheese or took calcium supplements everyday. 16.6% did some form of weight bearing exercise at least once a week. CONCLUSION: A local reference database is needed for the accurate interpretation of BMD measurements as there is significant variation compared to Caucasian values.

Absorptiometry, Photon↗
PubMed1999

18F-FDG PET studies in patients with extratemporal and temporal epilepsy: evaluation of an observer-independent analysis.

UNLABELLED: The aim of this study was to evaluate an observer-independent analysis of 18F-fluorodeoxyglucose (FDG) PET studies in patients with temporal or extratemporal epilepsy. METHODS: Twenty-seven patients with temporal epilepsy and 22 patients with extratemporal epilepsy were included in the study. All patients with temporal epilepsy and 7 patients with extratemporal epilepsy underwent surgical treatment. In patients who showed significant postoperative improvement (temporal, n = 23; extratemporal, n = 6), the epileptogenic focus was assumed to be located in the area of surgical resection. In extratemporal epilepsy patients who did not undergo surgery, the focus localization was determined using a combination of semiology, ictal and interictal electroencephalography, [99mTc]ethyl cysteinate dimer SPECT, MRI and [11C]flumazenil PET. Visual analysis was performed by two experienced and two less experienced blinded observers using sagittal, axial and coronal images. In the automated analysis after anatomic standardization and generation of three-dimensional stereotactic surface projections (SSPs), a pixelwise comparison of 18F-FDG uptake with an age-matched reference database (n = 20) was performed, resulting in z score images. Pixels with the maximum deviation were detected, summarized and attached to one of 20 predefined surface regions of interest. For comparison with 18F-FDG PET and MR images, three-dimensional overlay images were generated. RESULTS: In patients with temporal epilepsy, the sensitivity was comparable for visual and observer-independent analysis (three-dimensional SSP 86%, experienced observers 86%-90%, less experienced observers 77%-86%). In patients with extratemporal epilepsy, three-dimensional SSP showed a significantly higher sensitivity in detecting the epileptogenic focus (67%) than did visual analysis (experienced 33%-38%, each less experienced 19%). In temporal lobe epilepsy, there was moderate to good agreement between the localization found with three-dimensional SSP and the different observers. In patients with extratemporal epilepsy, there was a high interobserver variability and only a weak agreement between the localization found with three-dimensional SSP and the different observers. Although three-dimensional SSP detected multiple lesions more often than visual analysis, the determination of the highest deviation from the reference database allowed the identification of the epileptogenic focus with a higher accuracy than subjective criteria, especially in extratemporal epilepsy. CONCLUSION: Three-dimensional SSP increases sensitivity and reduces observer variability of the analysis of 18F-FDG PET images in patients with extratemporal epilepsy and is, therefore, a useful tool in the evaluation of this patient group. The benefit of this analytical approach in patients with temporal epilepsy is less apparent.

Adolescent↗
PubMed1996

Intralaboratory timeliness of surgical pathology reports. Results of two College of American Pathologists Q-Probes studies of biopsies and complex specimens.

OBJECTIVE: To develop multi-institutional reference databases for intralaboratory timeliness of surgical pathology routine biopsies and complex specimens from the time of specimen accessioning to report completion, and to examine the influence of laboratory characteristics and practices on turnaround time (TAT). DESIGN: Participants in the Q-Probes quality improvement program of the College of American Pathologists took part in two separate studies, the first conducted in 1992 and 1993 and the second in 1993 and 1994. Each participant tracked the number of days from specimen accessioning to report completion for 30 routine biopsies and 30 complex specimens in each study. Based on this intralaboratory time interval, performance was compared with the College of American Pathologists' laboratory accreditation standard of 2 working days. PARTICIPANTS: Five hundred twenty-five surgical pathology laboratories responded to the study of routine biopsies, and 489 laboratories responded to the study of complex specimens. Participants were mainly located in the United States, but there were respondents from Canada, Australia, New Zealand, and Hong Kong as well. RESULTS: In the first study, evaluation of 15 725 biopsy cases showed that the cumulative aggregate percentage of routine biopsy cases processed from the time of specimen accessioning to report completion was 79% by 1 working day, 95% by 2 working days, and 98% by 3 working days. Individual participant's data revealed that all reports were completed by the second working day in 90% of the laboratories and by the third working day in 95% of laboratories. Factors that significantly contributed to increased report TAT included larger institutional size, a greater number of surgical pathologists, greater annual surgical pathology volume processed, technical processing resulting in delayed slide availability, pathology practices that integrated residency training, and reduced staffing levels of histotechnologists/technicians and transcriptionists. Shorter TATs were achieved in those institutions that had previously established a TAT goal for routine biopsy specimens. In the second study of 14 298 aggregate complex specimen cases, 68% required routine processing and 32% required special handling. Overall, 56% of all complex specimen reports were processed and completed in 1 working day, 81% in 2 working days, 91% in 3 working days, and 95% in 4 working days. On average, the percentage of cases processed and reports signed out in 2 working days or less was 80% for all complex specimen cases, 90% for routine cases, and 60% for special-handling cases. The mean of all participants' median TATs was 1.5 days (range 0-5 days) for complex specimens, 1.3 days (range 0-5 days) for cases requiring routine handling, and 2.6 days (range 0-13.5 days) for cases requiring special handling. Several factors were associated with increased report TAT: institutional occupied bedsize greater than 450, routine responsibility for gross dissection assigned to residents only, earliest availability of slides after 12 pm, resident involvement in sign-out, interposing a day between availability of slides and final slide sign-out for resident education purposes, and a greater number of surgical pathologists. CONCLUSIONS: We have documented that for the majority of routine cases, the College of American Pathologists Laboratory Accreditation Program's TAT standard of report completion time within 2 working days for the intralaboratory component of TAT is a reasonable goal. This standard was successfully met by participants in 95% of routine biopsy cases and 91% of routine complex specimens. Special-handling procedures for complex specimens contributed, on average, an additional delay of 1.3 days. To our knowledge these are the first systematic studies to describe timeliness from the time of specimen accessioning to report completion for surgical pathology specimens, and they may serve as reference databases for benchm

Biopsy↗
PubMed1993

The forensic significance of various reference population databases for estimating the rarity of variable number of tandem repeat (VNTR) loci profiles.

The likelihood of occurrence of 1,964-HaeIII-generated target DNA profiles was estimated using fixed bin VNTR frequencies from various Caucasian, Black, and Hispanic databases and the product rule. The data in this study demonstrate that for forensic purposes there are smaller differences in statistical estimates of DNA profile frequencies among subgroup databases than among estimates across major population databases. This observation does not support the premise asserted by the NCR Report (1992) that the differences among subgroups within a race would be greater than between races (at least for forensic purposes). Therefore, the data do not support the need for alternative procedures, such as the ceiling principle approach (NRC Reports, 1992), for deriving statistical estimates of DNA profile frequencies. Comparisons across major population groups provide reasonable, reliable, and meaningful estimates of DNA profile frequencies without forensically significant consequences.

Black People↗
PubMed1990

On dividing reference data into subgroups to produce separate reference ranges.

We consider statistical criteria for partitioning a reference database to obtain separate reference ranges for different subpopulations. Using general formulas relating population variances, sample sizes, and the normal deviate test for the significance of the difference between two subgroup means, we show that partitioning into separate ranges produces little reduction in between-person variability, even when the differences between means are highly significant statistically. However, when there is a clear physiological basis for distinguishing between certain subgroups, simulation studies show that partitioning may be necessary to obtain reference limits that cut off the desired proportions of low and high values in each subgroup. Guidelines based on these results are provided to help decide whether separate ranges should be obtained for a given analyte.

Analysis of Variance↗
PubMed1994

A portable search engine and browser for the Entrez database.

Entrez is a molecular sequence and reference database. We present a tool called CLEVER which permits flexible access to the Entrez database by other applications and interactively by users. In this way, CLEVER is both a search engine and a command-line browser of the Entrez database.

Computer Communication Networks↗
PubMedDate not supplied

Approaching the millennium: perinatal problems and software solutions.

Strategic planning for rational development of perinatal computing capabilities for the year 2000 should be driven by anticipated trends in (1) the health care business, (2) computer technology and (3) medicine, as well as (4) the needs of perinatal practitioners. In the USA, health care is the fastest growing segment of the economy. This will produce increasing attention from hardware and software developers, and vendors, and will lead to a proliferation of computing platforms, operating systems and specific medical application software. Desktop computers, already capable of 20 million instructions per second (MIPS) with massive storage capacities, will continue to evolve and fall in price. Increasingly, perinatologists will develop software packages to facilitate patient care in their own environments. All of these trends will lead to severe fragmentation in medical computing. Simultaneously, however, the need for integrated institutional computer-based data access for quality assurance and fiscal and operations management will increase. Perinatal care will be more regionalized, complex and rigorous with new clinical trial- and effectiveness research-based interventions, as well as molecular diagnosis and therapy. To practice appropriately, clinicians will need to be familiar with computer capabilities. Having been exposed to computer-aided instruction (CAI) at the undergraduate and postgraduate levels, they will except on-line access to detailed and accurate patient information with linkage to laboratory, radiology and other medical databases, as well as to reference databases, such as Medlines and the Oxford Database of Perinatal Trials. Artificial intelligence (AI) software may support perinatal decision making; computerized professional and facility billing will be available.

Forecasting↗
PubMed1992

A profile for molecular biology databases and information resources.

This paper examines the requirements for building database management systems and multi-database information resources to support molecular biology research. The paper profiles the most important features of 16 integrated resources and 102 databases related to molecular biology research. The aspects surveyed in this paper include the nature of information in these databases, their sizes, update properties, cross-references, database management system heterogeneity, geographical distribution, data quality, use of temporal information and level of interpretation. The paper also comments on the access patterns to these databases. Since not all these aspects were available for all databases, specific comparisons sometimes compare fewer than the full 102 databases. Consequently, the same set of databases is not necessarily always being compared with respect to every aspect. The paper is organized primarily according to these comparison aspects and ends with some concluding remarks.

Databases, Bibliographic↗
PubMed2026

CamK-DB: A k-mer MinHash fingerprint database for reference-free genotyping of Camellia accessions.

Tea (Camellia sinensis L.), a major global economic crop in Asia, poses challenges for genetic identification because its highly heterozygous, repetitive genome reduces the efficacy of conventional single-nucleotide polymorphism (SNP) and microsatellite markers, and interspecific hybridization further complicates the situation. To address these issues, CamK-DB was developed as a reference-free Camellia fingerprinting database built on MIKE MinHash sketches. We curated 418 candidate resequencing datasets, and built a database using standardized 5× genome-coverage fingerprints. Each accession is stored as a MIKE. jac fingerprint generated with k = 21 and recommended sketch/pre_cnt = 2000. CamK-DB provides a command-line interface for data management and a custom C++ query engine that computes top-10 matches using Jaccard similarity, complemented by a QT-based graphical interface for interactive analysis. This resource offers a robust and scalable framework for precise and routine germplasm identification, genomic phylogenetic inference, and strategic breeding program design. CamK-DB (database and code) is publicly available at https://github.com/sc-zhang/CamK-DB. CamK-DB binaries are provided for Windows 10/11 and Linux (x86_64, glibc ≥ 2.27).

Databases, Genetic↗
PubMed1994

User-definable bull's-eye database analysis.

Several quantitative bull's-eye database programs have been developed and employed successfully, but generally they restrict the user to limited types of quantitative analysis. We developed a type of bull's-eye analysis which facilitates user-defined processing, and then explored the effects of various types of processing on the comparisons of patient information with that of reference databases. Male and female bull's-eye database were generated from 32 normal patients using unweighted 2D prefiltering, ramp backprojection, unweighted 3D postfiltering, and peak value circumferential plotting (base method). The data from each patient were then reprocessed and compared to the databases by means of three different approaches: (1) using the base method, (2) using average as opposed to peak value profiles, and (3) using a resolution recovery prefilter instead of a smoothing prefilter. Significant differences in the number of apparently abnormal regions were found between the three methods. In other words, the type of single-photon emission tomography (SPET) processing affected the accuracy of comparisons between patient and database information. Because even sophisticated analysis can now be performed on personal computers, we conclude that, rather than a preprocessed data file, clinical "normal reference" information should consist of original SPET data (in a standard format, e.g., Interfile) from a series of documented normal patients. Each user could then generate reference bull's-eye database by applying his or her own clinical processing procedures to the data.

Humans↗
PubMed1995

[Information sources on carcinogenic agents].

This work comprises lists of publications and computer data bases available at the Scientific Information Department, The Nofer Institute of Occupational Medicine, Lodz, Poland, containing information on cancer risks resulting from exposure to carcinogenic agents. The following publications have been described: IARC Monographs on the Evaluation of Carcinogenic Risk to Humans; Official lists of carcinogens valid in individual countries; a periodical--Survey of compounds which have been tested for carcinogenic activity; a guide--The Annual Report on Carcinogens, a series on Carcinogens in the Occupational Environment, comprising Information Cards and Monographs; a guide on Carcinogenic Agents, and computer databases, including the INCAR, IRIS, IRPTC, RTECS CHEMINFO factual databases and the CANCER-CD, MEDLINE, TOXLINE, NIOSHTIC and MEDIP bibliographic (or reference) databases. The presented publications and databases may prove helpful in searching for data on identifying and preventing the adverse health effects of environmental and occupational exposure to carcinogens.

Carcinogens↗
PubMedDate not supplied

[Electroconvulsive therapy and benzodiazepine: antagonism or indifference? Review of the literature].

BACKGROUND: It is usually considered that the efficacy of electroconvulsive therapy is due to the induction of a seizure (20). Benzodiazepines are well known antiepileptics (11) and it is suggested that they should be withdrawn during electroconvulsive therapy (3). The purpose of our study was to determine the evidence that exists for this hypothesis in the literature. METHOD: We have reviewed the international literature on electroconvulsive therapy and benzodiazepines through the Medline and Pascal reference database, and performed a manual search of the major international journals. We have retained the references dealing with both benzodiazepine and electroconvulsive therapy. RESULTS: Up to June 1990, 16 references have been found (table I). Of these 16 references, 5 (6, 7, 12, 19, 25) are letters to the editor with no data reported. Six papers (1, 2, 8, 9, 14, 22) examine benzodiazepines as anesthetics and only focus on anesthetic variables, ignoring electroconvulsive therapy-treatment outcome. Only four studies (5, 17, 23, 24) actually examine the incidence of benzodiazepine use on electroconvulsive therapy. Of these, three studies (17, 23, 24) report the incidence of benzodiazepines used as tranquilizers or hypnotics on duration of the electroconvulsive therapy induced seizure. One is a retrospective study (24) showing a decrease in seizure duration due to benzodiazepine use. Of the two prospective studies one shows (23) no difference in seizure duration and the other one (17) a decrease. These studies, however, fail to actually examine how the antidepressive efficacy of electroconvulsive therapy is modified by benzodiazepine use. One recent study (5) measures the antidepressive efficacy of electro-convulsive therapy through the decrease of a validated depression scale. This is a randomized double-blind study examining a short acting benzodiazepine used as an anesthetic in lieu of methohexital. Electroconvulsive therapy efficacy does not appear impaired. CONCLUSION: From our review of the literature it appears that the supposed negative effect of benzodiazepines on the antidepressive action of electroconvulsive therapy has not been demonstrated. Further studies are necessary warranted.

Anti-Anxiety Agents↗
PubMedDate not supplied

[International bibliographic databases--Current Contents on disk and in FTP format (Internet): presentation and guide].

This paper aims to provide technical and practical advice about finding references using Current Contents on disk (Macintosh or PC) or via the Internet (FTP). Seven editions are published each week. They are all organized in the same way and have the same search engine. The Life Sciences edition, extensively used in medical research, is presented here in detail, as an example. This methodological note explains, in French, how to use this reference database. It is designed to be a practical guide for browsing and searching the database, and particularly for creating search profiles adapted to the needs of researchers.

CD-ROM↗
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↗