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PubMed1999

Infant mortality statistics from the 1997 period linked birth/infant death data set.

OBJECTIVES: This report presents 1997 period infant mortality statistics from the linked birth/infant death data set (linked file) by a wide variety of maternal and infant characteristics. METHODS: Descriptive tabulations of data are presented. RESULTS: In general, mortality rates were lowest for infants born to Asian and Pacific Islander mothers (5.0), followed by white (6.0), American Indian (8.7), and black (13.7) mothers. Infant mortality rates were higher for Puerto Rican mothers (7.9) than for Mexican (5.8), Cuban (5.5), Central and South American (5.5), or non-Hispanic white mothers (6.0). Infant mortality rates were higher for those infants whose mothers began prenatal care after the first trimester of pregnancy, were teenagers or 40 years of age or older, did not complete high school, were unmarried, or smoked during pregnancy. Infant mortality was also higher for male infants, multiple births, and infants born preterm or at low birthweight. In 1997, 65 percent of all infant deaths occurred to the 7.5 percent of infants bom at low birthweight. The three leading causes of infant death--Congenital anomalies, Disorders relating to short gestation and unspecified low birthweight (low birthweight), and Sudden infant death syndrome (SIDS) taken together accounted for nearly one-half of all infant deaths in the United States in 1997. Cause-specific mortality rates varied considerably by race and Hispanic origin. For black mothers, the infant mortality rate for low birthweight was four times that for white mothers. For American Indian mothers, the SIDS rate was 2.4 times that for white mothers. For Hispanic mothers, the SIDS rate was one-third lower than that for non-Hispanic white mothers.

Adolescent↗

PubMed2002

Normalizing DNA microarray data.

DNA microarrays are a powerful tool to investigate differential gene expression for thousands of genes simultaneously. Although DNA microarrays have been widely used to understand the critical events underlying growth, development, homeostasis, behavior and the onset of disease, the management of the resulting data has received little attention. Presently, the fluorescent dyes Cy3 and Cy5 are most often used to prepare labeled cDNA for microarray hybridizations. Raw microarray data are image files that have to be transformed into gene expression formats--a process that requires data manipulation due to systematic variations which may be attributed to differences in the physical and chemical dye applications is to identify differences in transcript levels calculated from fluorescence ratios it is necessary to normalize fluorescence signals to compensate for systematic variations. Here, we will review current normalization strategies applied to cDNA microarrays and discuss their limits. We will show that experimental design determines normalization success.

Animals↗

PubMed2004

A study of determinants of low birth weight in Abha, Saudi Arabia.

This study examined the role of women's work as a possible determinant (among others) of low birth weight in the population of women followed in a Primary Health Care (PHC) center in Abha, Southern Saudi Arabia. All antenatal care files for all deliveries in the preceding 5 years were studied and the relevant data from 7067 files were collected and analyzed. Low birth weight was significantly higher in working mothers (odds ratio=1.31), adolescent mothers (odds ratio= 2.56), and low parity mothers (OR= 1.28). Anemia of the mother contributed an odds ratio of 1.23 for low birth weight baby and inadequate antenatal care (less than 3 visits during pregnancy) had an odds ratio of 1.9. Female babies were significantly more prone to low birth weight (odds ratio 1.34). It is suggested that further evaluation of women's work conditions to detect and remedy stressful conditions especially during pregnancies, health education and better antenatal care may prevent a good proportion of low birth weight deliveries.

Adolescent↗

PubMed1984

Data-base management system on a CT scanner computer: application to teaching file and procedure records.

A prototype relational data-base management system was installed on computed tomographic (CT) scanner computers at two hospitals. This was used to create computerized indices for a teaching file and a record of CT procedures. Several problems commonly encountered when maintaining and using a radiologic teaching file were solved. Interesting cases were easily retrieved for teaching, conferences, or publication because the system permits rapid search on the basis of patient name, identification number, date, diagnosis, special description, or a combination of these data. The procedure record index contains these data as well as administrative and technical data on all CT examinations. These data are entered into the data base semiautomatically. The result is an extensive set of records that is easily accessible and requires a minimum of manpower to maintain.

Computers↗

PubMed2003

The tissue microarray data exchange specification: a community-based, open source tool for sharing tissue microarray data.

BACKGROUND: Tissue Microarrays (TMAs) allow researchers to examine hundreds of small tissue samples on a single glass slide. The information held in a single TMA slide may easily involve Gigabytes of data. To benefit from TMA technology, the scientific community needs an open source TMA data exchange specification that will convey all of the data in a TMA experiment in a format that is understandable to both humans and computers. A data exchange specification for TMAs allows researchers to submit their data to journals and to public data repositories and to share or merge data from different laboratories. In May 2001, the Association of Pathology Informatics (API) hosted the first in a series of four workshops, co-sponsored by the National Cancer Institute, to develop an open, community-supported TMA data exchange specification. METHODS: A draft tissue microarray data exchange specification was developed through workshop meetings. The first workshop confirmed community support for the effort and urged the creation of an open XML-based specification. This was to evolve in steps with approval for each step coming from the stakeholders in the user community during open workshops. By the fourth workshop, held October, 2002, a set of Common Data Elements (CDEs) was established as well as a basic strategy for organizing TMA data in self-describing XML documents. RESULTS: The TMA data exchange specification is a well-formed XML document with four required sections: 1) Header, containing the specification Dublin Core identifiers, 2) Block, describing the paraffin-embedded array of tissues, 3)Slide, describing the glass slides produced from the Block, and 4) Core, containing all data related to the individual tissue samples contained in the array. Eighty CDEs, conforming to the ISO-11179 specification for data elements constitute XML tags used in the TMA data exchange specification. A set of six simple semantic rules describe the complete data exchange specification. Anyone using the data exchange specification can validate their TMA files using a software implementation written in Perl and distributed as a supplemental file with this publication. CONCLUSION: The TMA data exchange specification is now available in a draft form with community-approved Common Data Elements and a community-approved general file format and data structure. The specification can be freely used by the scientific community. Efforts sponsored by the Association for Pathology Informatics to refine the draft TMA data exchange specification are expected to continue for at least two more years. The interested public is invited to participate in these open efforts. Information on future workshops will be posted at http://www.pathologyinformatics.org (API we site).

Community Health Services↗

PubMed2006

A suite of Mathematica notebooks for the analysis of protein main chain 15N NMR relaxation data.

A suite of Mathematica notebooks has been designed to ease the analysis of protein main chain 15N NMR relaxation data collected at a single magnetic field strength. Individual notebooks were developed to perform the following tasks: nonlinear fitting of 15N-T1 and -T2 relaxation decays to a two parameter exponential decay, calculation of the principal components of the inertia tensor from protein structural coordinates, nonlinear optimization of the principal components and orientation of the axially symmetric rotational diffusion tensor, model-free analysis of 15N-T1, -T2, and {1H}-15N NOE data, and reduced spectral density analysis of the relaxation data. The principle features of the notebooks include use of a minimal number of input files, integrated notebook data management, ease of use, cross-platform compatibility, automatic visualization of results and generation of high-quality graphics, and output of analyses in text format.

Anisotropy↗

PubMed1991

Computerised transfer and processing of data from experiments measuring cellular proliferation by incorporation of tritiated thymidine.

One of the major endpoints of cellular immunological tests remains the quantitative assessment of lymphocyte proliferation as estimated from incorporation of tritiated thymidine into dividing cells. These data are usually generated by beta scintillation counting as strings of counts per minute which require considerable data reduction and processing. A computer system for the collection, transfer, presentation, processing and storage of these data is outlined here. This is based on modules operating from a basic system of maximal simplicity and flexibility in which data are stored in ASCII files and where the particular data processing requirements of different investigators can be easily met. This is exemplified by using a number of examples from the authors' own experiments, also illustrating the point that proliferative responses of non-lymphoid cells can be processed in the same way. In addition, suggestions are made concerning the standardisation of data processing for the exchange of results between different laboratories collaborating in large scale investigations, for example, the International Histocompatibility Workshops.

Diagnosis, Computer-Assisted↗

PubMedDate not supplied

ArrayExpress: a public database of gene expression data at EBI.

ArrayExpress is a public repository for microarray-based gene expression data, resulting from the implementation of the MAGE object model to ensure accurate data structuring and the MIAME standard, which defines the annotation requirements. ArrayExpress accepts data as MAGE-ML files for direct submissions or data from MIAMExpress, the MIAME compliant web-based annotation and submission tool of EBI. A team of curators supports the submission process, providing assistance in data annotation. Data retrieval is performed through a dedicated web interface. Relevant results may be exported to ExpressionProfiler, the EBI based expression analysis tool available online (http://www.ebi.ac.uk/arrayexpress).

Computational Biology↗

PubMed2004

The influence of rural location on utilization of formal home care: the role of Medicaid.

PURPOSE: This research examines the impact of rural-urban residence on formal home-care utilization among older people and determines whether and how Medicaid coverage influences the association between rural-urban location and risk of formal home-care use. DESIGN AND METHODS: We combined data from the 1998 consolidated file of the Medical Expenditure Panel Survey Household Component with data from the Area Resource File to generate the analytical data set. We established two measures of formal home-care utilization: home care reimbursed through any source, and Medicare-reimbursed home health care. Our measures of rural-urban residence included metropolitan counties, nonmetropolitan counties having towns of at least 10,000 people, and nonmetropolitan counties with no towns of 10,000 people. We used logistic regression analyses to examine main effects and interaction effects of Medicaid coverage and residence on the two types of formal home care under controls for person-level characteristics and state fixed effects. RESULTS: The unadjusted logistic analyses demonstrate that older people who reside in the most rural counties (nonmetropolitan counties having no town of 10,000) are significantly more likely than metropolitan residents to use any formal home care and Medicare home health care. The fully adjusted logistic analysis results point to an interplay between residential status and Medicaid coverage with regard to formal home-care use. In comparison with metropolitan residents covered by Medicaid, the adjusted relative risk of any formal home-care use is significantly higher for Medicaid enrollees residing in nonmetropolitan counties having no town of 10,000 people. Use of Medicare home health care is significantly greater for residents of the most rural counties, irrespective of their Medicaid coverage, as well as Medicaid-covered residents of nonmetropolitan counties having a town of at least 10,000 people. IMPLICATIONS: In nonmetropolitan areas, Medicaid may be an important mechanism for linking older individuals with formal home care, especially Medicare home health care, and with the services that generate formal home care. Formal home care, including Medicare home health care, may substitute for less available forms of care in the most rural of nonmetropolitan areas. Therefore, policies that limit access to formal home care could lead to increased service-related vulnerabilities among older rural residents.

Aged↗

PubMed2002

PipeOnline 2.0: automated EST processing and functional data sorting.

Expressed sequence tags (ESTs) are generated and deposited in the public domain, as redundant, unannotated, single-pass reactions, with virtually no biological content. PipeOnline automatically analyses and transforms large collections of raw DNA-sequence data from chromatograms or FASTA files by calling the quality of bases, screening and removing vector sequences, assembling and rewriting consensus sequences of redundant input files into a unigene EST data set and finally through translation, amino acid sequence similarity searches, annotation of public databases and functional data. PipeOnline generates an annotated database, retaining the processed unigene sequence, clone/file history, alignments with similar sequences, and proposed functional classification, if available. Functional annotation is automatic and based on a novel method that relies on homology of amino acid sequence multiplicity within GenBank records. Records are examined through a function ordered browser or keyword queries with automated export of results. PipeOnline offers customization for individual projects (MyPipeOnline), automated updating and alert service. PipeOnline is available at http://stress-genomics.org.

Automation↗

PubMed2001

Complete 3-D reconstruction of dental cast shape using perceptual grouping.

To achieve the complete three-dimensional (3-D) data retrieval of the shape of dentition, dental casts were measured from four directions; occlusal, right, left, and labial sides using a line laser scanner. Reconstruction of the entire shape, including undercuts and tooth crowding area, was attempted by applying a perceptual grouping algorithm, which is one of pattern-recognition theories. In the data measured from occlusal, right and left sides, the rows of measurements were parallel to the frontal plane, and three-directionally combined data (3-DC data) was accomplished by affine transformation. While, in the labial side, transformation to the frontal plane was done since rows of the measured data were parallel to the sagittal plane. To combine the labial data with the 3-DC data and reconstruct the complete image, rearrangement of the order of the data in the file was attempted by applying the perceptual grouping. That is, the minimum total length of data combining was examined by considering the factor of proximity and continuity between the data. The most appropriate order of data combining and recognition of islands were accomplished. Using a computer graphic (CG) with a wire-frame model, complicated regions such as anterior segments showing tooth crowding and undercut area were found to be successfully reconstructed without any data defects. The accuracy of reconstruction was ascertained by comparing the characteristic distances between apexes of molars in the reconstructed model with the real cast. The difference was within 0.3 mm, and present method for dental cast reconstruction is considered to be satisfactory for the present purpose such as orthodontics.

Dental Casting Technique↗

PubMed2003

Working more productively: tools for administrative data.

OBJECTIVE: This paper describes a web-based resource (http://www.umanitoba.ca/centres/mchp/concept/) that contains a series of tools for working with administrative data. This work in knowledge management represents an effort to document, find, and transfer concepts and techniques, both within the local research group and to a more broadly defined user community. Concepts and associated computer programs are made as "modular" as possible to facilitate easy transfer from one project to another. STUDY SETTING/DATA SOURCES: Tools to work with a registry, longitudinal administrative data, and special files (survey and clinical) from the Province of Manitoba, Canada in the 1990-2003 period. DATA COLLECTION: Literature review and analyses of web site utilization were used to generate the findings. PRINCIPAL FINDINGS: The Internet-based Concept Dictionary and SAS macros developed in Manitoba are being used in a growing number of research centers. Nearly 32,000 hits from more than 10,200 hosts in a recent month demonstrate broad interest in the Concept Dictionary. CONCLUSIONS: The tools, taken together, make up a knowledge repository and research production system that aid local work and have great potential internationally. Modular software provides considerable efficiency. The merging of documentation and researcher-to-researcher dissemination keeps costs manageable.

Databases as Topic↗

PubMed2004

Monitoring visual status: why patients do or do not comply with practice guidelines.

OBJECTIVE: To determine factors affecting compliance with guidelines for annual eye examinations for persons diagnosed with diabetes mellitus (DM) or age-related macular degeneration (ARMD). DATA SOURCES/STUDY SETTING: Nationally representative, longitudinal sample of individuals 65+ drawn from the National Long-Term Care Survey (NLTCS) with linked Medicare claims records from 1991 to 1999. STUDY DESIGN: Medicare beneficiaries were followed from 1991 to 1999, unless mortality intervened. All claims data were analyzed for presence of ICD-9 codes indicating diagnosis of DM or ARMD and the performance of eye exams. The dependent variable was a binary indicator for whether a person had an eye exam or not during a 15-month period. Independent variables for demographics, living conditions, supplemental insurance, income, and other factors affecting the marginal cost and benefit of an eye exam were assessed to determine reasons for noncompliance. DATA COLLECTION/EXTRACTION METHODS: Panel data were created from claims files, 1991-1999, merged with data from the NLTCS. PRINCIPAL FINDINGS: The probability of having an exam reflected perceived benefits, which vary by patient characteristics (e.g., education, no dementia), and factors associated with the ease of visit. African Americans were much less likely to be examined than were whites. CONCLUSIONS: Having an exam reflects multiple factors. However, much of the variation in the probability of an exam remained unexplained as were reasons for the racial differences in use.

Aged↗

PubMed2005

The safety of herbal medicinal products derived from Echinacea species: a systematic review.

Echinacea spp. are native to North America and were traditionally used by the Indian tribes for a variety of ailments, including mouth sores, colds and snake-bites. The three most commonly used Echinacea spp. are E. angustifolia, E. pallida and E. purpurea. Systematic literature searches were conducted in six electronic databases and the reference lists of all of the papers located were checked for further relevant publications. Information was also sought from the spontaneous reporting programmes of the WHO and national drug safety bodies. Twenty-three manufacturers of echinacea were contacted and asked for data held on file. Finally our own departmental files were searched. No language restrictions were imposed. Combination products and homeopathic preparations were excluded. Data from clinical studies and spontaneous reporting programmes suggest that adverse events with echinacea are not commonly reported. Gastrointestinal upsets and rashes occur most frequently. However, in rare cases, echinacea can be associated with allergic reactions that may be severe. Although there is a large amount of data that investigates the efficacy of echinacea, safety issues and the monitoring of adverse events have not been focused on. Short-term use of echinacea is associated with a relatively good safety profile, with a slight risk of transient, reversible, adverse events. The association of echinacea with allergic reactions is supported by the present evaluation. While these reactions are likely to be rare, patients with allergy or asthma should carefully consider their use of echinacea. The use of echinacea products during pregnancy and lactation would appear to be ill-advised in light of the paucity of data in this area.

Adult↗

PubMedDate not supplied

The epidemiological information system of the French national electricity and gas company: the SI-EPI project.

SI-EPI is epidemiological information system set up in 1978 in the national electricity and gas company, Electricité de France-Gaz de France (EDF-GDF). The worker population comprises about 150,000 individuals, involved in production, transmission and distribution of energy. SI-EPI was developed by the epidemiologists of the Occupational Health Department (180 physicians), and of the Sécurité Sociale Department (120 physicians). Several data bases constitute SI-EPI. The population data base contains demographic, socioeconomic and professional data about each worker. The health data base is an exhaustive register of sick leave, accidents, permanent disabilities, compensated diseases, causes of death and cancer incidence among active workers. The Occupational Exposure and Working Conditions data base includes the MATEX job-exposure matrix (30 potentially carcinogenic agents) and FINDEX files which record data obtained from the systematic individual surveillance of workers. The GAZEL cohort data base concerns a sample of more than 20,000 volunteer workers, followed since 1989; in addition to data from the data bases, it contains information collected from other different sources, including self-questionnaires. Numerous epidemiological studies based on SI-EPI data have been conducted by in-house epidemiologists as well as by external research groups. They include mortality and morbidity studies and address various topics and health problems. Their results are used for internal information, as well as for epidemiological research purposes.

Adult↗

PubMed2001

A metadata framework for interoperating heterogeneous genome data using XML.

The rapid advances in the Human Genome Project and genomic technologies have produced massive amounts of data populated in a large number of network-accessible databases. These technological advances and the associated data can have a great impact on biomedicine and healthcare. To answer many of the biologically or medically important questions, researchers often need to integrate data from a number of independent but related genome databases. One common practice is to download data sets (text files) from various genome Web sites and process them by some local programs. One main problem with this approach is that these programs are written on a case-by-case basis because the data sets involved are heterogeneous in structure. To address this problem, we define metadata that maps these heterogeneously structured files into a common eXtensible Markup Language (XML) structure to facilitate data interoperation. We illustrate this approach by interoperating two sets of essential yeast genes that are stored in two yeast genome databases (MIPS and YPD).

Databases, Genetic↗

PubMed2000

MAD: a suite of tools for microarray data management and processing.

SUMMARY: Microarray data management and processing (MAD) is a set of Windows integrated software for microarray analysis. It consists of a relational database for data storage with many user-interfaces for data manipulation, several text file parsers and Microsoft Excel macros for automation of data processing, and a generator to produce text files that are ready for cluster analysis. AVAILABILITY: Executable is available free of charge on http://pompous.swmed.edu. The source code is also available upon request.

Databases, Factual↗

PubMedDate not supplied

A systematic review of the safety of black cohosh.

OBJECTIVE: To systematically review the available data relating to the safety of medicinal extracts of black cohosh (Actaea racemosa). DESIGN: Systematic literature searches were conducted in seven electronic databases, and the reference lists of all papers located were checked for further relevant publications. Information was also sought from the spontaneous reporting programs of the World Health Organization and national drug safety bodies. Sixteen manufacturers of black cohosh preparations were contacted and asked for data held on file. Finally, our own departmental files were searched. No language restrictions were imposed. Combination products and homeopathic preparations were excluded. RESULTS: Data from clinical studies and spontaneous reporting programs suggest that adverse events (AEs) with black cohosh are rare, mild, and reversible. Gastrointestinal upsets and rashes are the most common AEs. The spontaneous reporting programs do contain a few serious AEs, including hepatic and circulatory conditions, but causality cannot be determined. Although there is large amount of data investigating the efficacy of black cohosh, in particular the product Remifemin, safety issues and the monitoring of AEs have not been the focus. CONCLUSION: If black cohosh products are taken for a limited length of time, there seems to be a slight risk of mild, transient AEs. More serious AEs seem to be rare, and it is impossible to ascertain causality with black cohosh with the limited data available. Thus, although definitive evidence is not available, it would seem that black cohosh is a safe herbal medicine.

Cimicifuga↗