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PubMed2025

Consistently processed RNA sequencing data from 50 sources enriched for pediatric data.

Larger cohorts improve the power of tumor gene expression analysis, but the signal is muddied if datasets are processed using different methods or have inaccurate metadata. Here we present five compendia containing consistently processed gene expression data derived from 16,446 diverse RNA sequencing datasets. To create the compendia, we obtained access to RNA sequence data from repositories containing public data as well as clinical partners with access to non-published data. We then assessed the quality, quantified gene expression, harmonized clinical metadata, and released the expression values and metadata without access restrictions. These datasets have been used for diverse projects ranging from identifying similarities between tumor types to assessing how well cell lines recapitulate tumors. They have also been used for n-of-1 analysis to identify genes with unusual expression patterns in a single sample and to infer molecular diagnosis. The comparison to new data is enabled by our dockerized, freely available pipeline. The compendia have been cited in at least 20 publications.

Humans↗
PubMed1993

An object model for uniform access to heterogeneous databases.

The vast amount of patient information collected and maintained by hospitals is seldom stored in a single database. Much programming effort is wasted on formulating specific queries for each of several data sources, rather than focusing attention on developing the intended functionality of the application. This problem becomes more apparent as more data sources become available. The most obvious strategy for dealing with this multiplicity of data sources, namely storing all data in a single database, is impractical for reasons such as security and administrative control. This paper describes one possible solution to managing access to several database systems within applications. Using object-oriented techniques, the solution identifies the commonality among database management systems and provides a uniform method of communication between applications and databases. We describe a C(++)-based implementation which embodies these concepts.

Computer Communication Networks↗
PubMed2005

Epidemiology of MDMA and associated club drugs in the Seattle area.

Club drug use, MDMA in particular, appeared as a growing problem in the Seattle area in the late 1990s. To understand more about the patterns of MDMA use and to evaluate the current state of MDMA use, multiple data sources were examined. The seven data sources utilized included local community-based club drug surveys collected in 2003 at raves, treatment agencies, and gay-oriented bars and sex clubs; school surveys (collected in 2002); mortality data (deaths between 2000 and 2002); data from the sexually transmitted disease clinic (October 2002 to October 2003); focus groups (2003) with men who have sex with men; emergency department drug mentions (1995 to 2002); and drug treatment admissions (1999 to 2003). Taken together, these data indicate moderate levels of MDMA use and relatively low levels of mortality and acute morbidity. However, there are several areas of concern including possible mental health effects and high levels of suspected adulteration of MDMA. Some data point to a relationship between MDMA use and risky behaviors including unprotected sex. Implications for prevention, intervention, and treatment are discussed.

Adolescent↗
PubMed2000

Identification of resource use and associated costs for viral meningitis.

PURPOSE: This study involved identifying resource use and assigning monetary value to the diagnostic work-up and management of viral meningitis. METHODOLOGY: Using a previously established decision analytic framework, various resources were identified as part of routine management of viral meningitis. Secondary database analyses were used to quantify resources and assign a monetary value as a part of routine management of viral meningitis requiring use of the resource units identified in the decision analytic framework. Discharge data sources from the states of California, Florida, and Illinois, and Medicaid data sources from the state of Pennsylvania, were used for the purpose of analysis. PRINCIPAL FINDINGS: Physician visits, emergency room visits, hospital admissions, procedures, and medications were identified as the major resource used. Lumbar punctures, CT scans, and antibiotics were identified as the major procedures and medications utilized. No significant difference was found in the major resources used between the states' discharge data and the Medicaid data sources. The mean total charges for patient admissions with CT scans were significantly higher than for patient admissions without CT scans ($11,531.80 vs $7,841.30, P < 0.05). The mean lengths of stay for patients with CT scan were significantly higher than for patient admissions without CT scans (4.71 days vs. 3.88 days, P < 0.05). The patient readmission rate was 10.7 percent, while the readmission rate for episodes with more than one hospitalization was 11.1 percent. The mean charge associated with readmission was $12,200.

Decision Support Systems, Clinical↗
PubMed2005

Dental procedures can be undertaken without alteration of oral anticoagulant regimen.

DATA SOURCES: Medline provided the primary data source with references from identified articles being reviewed for additional studies. The Cochrane Collaboration database was also searched and a search performed of cited references. STUDY SELECTION: Clinical studies, in English, examining perioperative management of patients receiving long-term oral anticoagulant (OAC) therapy were selected. DATA EXTRACTION AND SYNTHESIS: Data were extracted regarding management strategy, thrombo-embolic events and bleeding complications, and type of surgical or invasive procedure. Event rates were reported as number of patients experiencing the event divided by number of patients at risk. Binomial and Poisson distributions were used to calculate 95% confidence intervals (CI). RESULTS: A total of 31 reports were identified and concluded to be of generally poor quality. For studies reporting thrombo-embolic events, 29 events occurred in 1868 patients (1.6%; 95% CI, 1.0-2.1) of which seven were strokes (0.4%; 95% CI, 0.0-0.7). Major bleeding while receiving OAC was reported to be rare for dental procedures (occurring in four out of 2014 individuals), arthrocentesis (in none out of 32), cataract surgery (none out of 203), and upper endoscopy or colonoscopy with or without biopsy (no occurrences in 111 patients). For the other invasive and surgical procedures reviewed, OAC needs to be withheld and a suitable personalised perioperative management strategy instigated. A guideline, based on the limited evidence available, for the perioperative management of anticoagulation for procedures requiring discontinuation of OAC is presented. CONCLUSIONS: Certain surgical or invasive procedures can be undertaken in patients who are taking OAC therapy without alteration of their regimen. For procedures requiring discontinuation of OAC, personalised management strategies are required. More rigorous studies are needed to better inform this debate.

Comment↗
PubMedDate not supplied

Problem-oriented prefetching for an integrated clinical imaging workstation.

Prefetching methods have traditionally been used to restore archived images from picture archiving and communication systems to diagnostic imaging workstations prior to anticipated need, facilitating timely comparison of historical studies and patient management. The authors describe a problem-oriented prefetching scheme, detailing 1) a mechanism supporting selection of patients for prefetching via characterizations of clinical problems, using multiple data sources (picture archiving and communication systems, hospital information systems, and radiology information systems), classifying patients into cohorts on the basis of their medical conditions (e.g., lung cancer); and 2) prefetching of multimedia data (imaging, laboratory, and medical reports) from clinical databases to enable the viewing of an integrated patient record. Preliminary evaluation of the prefetching algorithm using classic information retrieval measures showed that the system had high recall (100 percent), correctly identifying and retrieving data for all patients belonging to a target cohort, but low precision (50 percent). A key finding during testing was that the recall of the system was increased through the use of multiple data sources (compared with one data source), because of better patient descriptors. Medical problems and patient cohorts were more specifically defined by combining information from heterogeneous databases.

Algorithms↗
PubMed1997

Mortality by cause for eight regions of the world: Global Burden of Disease Study.

BACKGROUND: Reliable information on causes of death is essential to the development of national and international health policies for prevention and control of disease and injury. Medically certified information is available for less than 30% of the estimated 50.5 million deaths that occur each year worldwide. However, other data sources can be used to develop cause-of-death estimates for populations. To be useful, estimates must be internally consistent, plausible, and reflect epidemiological characteristics suggested by community-level data. The Global Burden of Disease Study (GBD) used various data sources and made corrections for miscoding of important diseases (eg, ischaemic heart disease) to estimate worldwide and regional cause-of-death.patterns in 1990 for 14 age-sex groups in eight regions, for 107 causes. METHODS: Preliminary estimates were developed with available vital-registration data, sample-registration data for India and China, and small-scale population-study data sources. Registration data were corrected for miscoding, and Lorenz-curve analysis was used to estimate cause-of-death patterns in areas without registration. Preliminary estimates were modified to reflect the epidemiology of selected diseases and injuries. Final estimates were checked to ensure that numbers of deaths in specific age-sex groups did not exceed estimates suggested by independent demographic methods. FINDINGS: 98% of all deaths in children younger than 15 years are in the developing world. 83% and 59% of deaths at 15-59 and 70 years, respectively, are in the developing world. The probability of death between birth and 15 years ranges from 22.0% in sub-Saharan Africa to 1.1% in the established market economies. Probabilities of death between 15 and 60 years range from 7.2% for women in established market economies to 39.1% for men in sub-Saharan Africa. The probability of a man or woman dying from a non-communicable disease is higher in sub-Saharan Africa and other developing regions than in established market economies. Worldwide in 1990, communicable, maternal, perinatal, and nutritional disorders accounted for 17.2 million deaths, non-communicable diseases for 28.1 million deaths and injuries for 5.1 million deaths. The leading causes of death in 1990 were ischaemic heart disease (6.3 million deaths), cerebrovascular accidents (4.4 million deaths), lower respiratory infections (4.3 million), diarrhoeal diseases (2.9 million), perinatal disorders (2.4 million), chronic obstructive pulmonary disease (2.2 million), tuberculosis (2.0 million), measles (1.1 million), road-traffic accidents (1.0 million), and lung cancer (0.9 million). INTERPRETATION: Five of the ten leading killers are communicable, perinatal, and nutritional disorders largely affecting children. Non-communicable diseases are, however, already major public health challenges in all regions. Injuries, which account for 10% of global mortality, are often ignored as a major cause of death and may require innovative strategies to reduce their toll. The estimates by cause have wide Cls, but provide a foundation for a more informed debate on public-health priorities.

Adolescent↗
PubMed1995

Black/white differences in prenatal care utilization: an assessment of predisposing and enabling factors.

OBJECTIVE: This article reports on analysis of the predisposing and enabling factors that affect black/white differences in utilization of prenatal care services. DATA SOURCES: We use a secondary data source from a survey conducted by the Michigan Department of Public Health. STUDY DESIGN: The study uses multivariate analysis methods to examine black/white differences in (1) total number of prenatal care visits, (2) timing of start of prenatal care, and (3) adequacy of care received. We use the model advanced by Aday, Andersen, and Fleming (1980) to examine the effect of enabling and predisposing factors on black/white differences in prenatal care utilization. DATA COLLECTION: A questionnaire was administered to all women who delivered in Michigan hospitals with an obstetrical unit. PRINCIPAL FINDINGS: Enabling factors fully accounted for black/white differences in timing of start of prenatal care; however, the model could not fully account for black/white differences in the total number or the adequacy of prenatal care received. CONCLUSION: Although there are no black/white differences in the initiation of prenatal care, black women are still less likely to receive adequate care as measured by the Kessner index, or to have as many total prenatal care contacts as white women. It is possible that barriers within the health care system that could not be assessed in this study may account for the differences we observed. Future research should consider the characteristics of the health care system that may account for the unwillingness or inability of black women to continue to receive care once they initiate prenatal care.

Adult↗
PubMed2005

Longer orthodontic treatment may result in greater external apical root resorption.

DATA SOURCES: Medline was the primary data source, with references of identified papers then being reviewed for additional studies. STUDY SELECTION: Studies were included if they were clinical trials, in English, of samples of greater than 10 subjects who had undergone fixed appliance orthodontic treatment and who had both pre- and postoperative X-rays available. A measurement of external apical root resorption (EARR) in maxillary incisors was essential as was a measure of displacement with the apex of the root as reference. DATA EXTRACTION AND SYNTHESIS: Variables were coded and articles graded by three independent investigators who subsequently negotiated final coding and assessed the methodological soundness of each study. A cumulative 'meta-analysis factor' was computed for each article. Articles were evaluated on study design; population sample; treatment assignment; documentation of statistics; the accuracy of root resorption measurement and apical displacement of incisor roots. A funnel plot analysis did not identify publication bias. RESULTS: Eight articles were included in the statistical analysis. Two did not contain data for mean apical displacement and therefore correlations between mean EARR and mean apical displacement could not be calculated for them. The mean meta-analysis factor was 39 (range, 12-78). Mean root resorption was 1.421+/-0.448 mm (n=8), and mean apical displacement was 2.382+/-0.756 mm. The weighted correlation coefficient between mean root resorption and apical displacement was 0.822 and that between mean root resorption and treatment duration was 0.852. CONCLUSIONS: This analysis suggests that treatment-related root resorption is correlated with the distance the apex moves and the length of time the treatment took.

Comment↗
PubMed2005

Implementation of laboratory order data in BioSense Early Event Detection and Situation Awareness System.

INTRODUCTION: Laboratory test orders constitute an early outbreak data source. CDC receives laboratory order data in HL7 format from the Laboratory Corporation of America (LabCorp) and plans to use the data in the BioSense Early Event Detection and Situation Awareness System. METHODS: These LabCorp data contain information on tests ordered and include the type of test ordered and the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM)-coded reasons for the order. A consensus panel was formed to group test orders on the basis of expert opinion into eight standard syndrome categories to provide an additional data source for early outbreak detection. A laboratory order taxonomy was developed and used in the mapping consolidation phase. The five main classes of this taxonomy are miscellaneous functional tests, fluid screening tests, system-specific tests, tests for specific infections (by primary manifestation), and tests for specific noninfectious diseases. RESULTS: Summary of numbers of laboratory order codes in each syndrome category are fever (53), respiratory (53), gastrointestinal (27), neurological (35), rash (37), lymphadenitis (20), localized cutaneous lesion (11), and specific infection (63). CONCLUSION: With the daily use of laboratory order data in BioSense, the actual distribution of laboratory order codes in syndrome groups can be evaluated, allowing modification of the mapping.

Clinical Laboratory Information Systems↗
PubMed1993

Selection in a preferred provider organization enrollment.

OBJECTIVE: The study was conducted to determine whether favorable or adverse selection occurred in a preferred provider organization (PPO) enrollment. DATA SOURCES AND STUDY SETTING: Secondary data sources were used to conduct a retrospective study of the utilization of health services and the demographic characteristics of the population involved in the first open enrollment in a new university-based PPO. The PPO under study, sponsored by the University of Michigan (UM) Medical Center, was offered to all 43,005 UM employees, dependents, and retirees. STUDY DESIGN: We analyzed insurance company payments during the one-year period prior to the enrollment to compare the utilization patterns of those who enrolled in the PPO with those who did not. DATA COLLECTION: Prior health care utilization data were obtained from Blue Cross-Blue Shield of Michigan on the entire university population for one year prior to the start of the PPO. Demographic data were obtained from the personnel office of the university. PRINCIPAL FINDINGS: The PPO group had a younger median age than the non-PPO group; the sex distribution was roughly similar for the two groups. In the PPO group 57 percent of all contracts were family contracts compared with only 30 percent in the non-PPO group. The PPO group experienced 20.6 percent lower inpatient payments per member, and 9.4 percent lower outpatient payments per member in the year prior to the enrollment. These differences resulted in an overall 18.7 percent lower payment per member for the PPO group in the year prior to their enrollment. CONCLUSIONS: The results show, based on prior insurance payments, that this PPO received favorable selection during the open enrollment, a finding consistent with favorable selection found in early HMO enrollment.

Academic Medical Centers↗
PubMed2005

Impact of intercensal population projections and error of closure on breast cancer surveillance: examples from 10 California counties.

INTRODUCTION: In 2001, data from the California Cancer Registry suggested that breast cancer incidence rates among non-Hispanic white (nHW) women in Marin County, California, had increased almost 60% between 1991 and 1999. This analysis examines the extent to which these and other breast cancer incidence trends could have been impacted by bias in intercensal population projections. METHOD: We obtained population projections for the year 2000 projected from the 1990 census from the California Department of Finance (DOF) and population counts from the 2000 US Census for nHW women living in 10 California counties and quantified age-specific differences in counts. We also computed age-adjusted incidence rates of invasive breast cancer in order to examine and quantify the impact of differences between the population data sources. RESULTS: Differences between year 2000 DOF projections and year 2000 census counts varied by county and age and ranged from underestimates of 60% to overestimates of 64%. For Marin County, the DOF underestimated the number of nHW women aged 45 to 64 years by 32% compared to the 2000 US census. This difference produced a significant 22% discrepancy between breast cancer incidence rates calculated using the two population data sources. In Los Angeles and Santa Clara counties, DOF-based incidence rates were significantly lower than rates based on census data. Rates did not differ significantly by population data source in the remaining seven counties examined. CONCLUSION: Although year 2000 population estimates from the DOF did not differ markedly from census counts at the state or county levels, greater discrepancies were observed for race-stratified, age-specific groups within counties. Because breast cancer incidence rates must be calculated with age-specific data, differences between population data sources at the age-race level may lead to mis-estimation of breast cancer incidence rates in county populations affected by these differences, as was observed in Marin County. Although intercensal rates based on population projections are important for timely breast cancer surveillance, these rates are prone to bias due to the error of closure between population projections and decennial census population counts. Intercensal rates should be interpreted with this potential bias in mind.

Breast Neoplasms↗
PubMed2006

Interviews or medical records, which type of data yields the best information on elderly people's health status?

BACKGROUND AND AIMS: Self-reported data and/or medical records are often used to assess the prevalence of illness and impairment in epidemiological studies. However, these two data sources do not always provide the same information. The aim was to compare data from interviews and medical records regarding illness, symptoms and impairment in the elderly, and to analyze the agreement between a consensus from both data sources and data from interviews and medical records, respectively. METHODS: We interviewed 130 persons (age range 67-99) regarding socio-demographic background data and physical and mental health. Medical records were reviewed. Illness burden was rated according to the Cumulative Illness Rating Scale for Geriatrics, and was rated in three ways based on: (1) interview data; (2) medical records; (3) information from both interviews and medical records considered to be consensus. Agreement was measured by the Kappa coefficient and the Svensson Paired Rank Measurement. A permutation test tested whether the ratings from interviews and medical records had the same agreement when compared with consensus. RESULTS: Statistically significant differences in agreement were found between interview versus consensus and medical records versus consensus for the vascular system (medical records best), eyes/ears/nose/throat/larynx and musculoskeletal/integument (interview best). Medical records gave better in formation concerning specific diseases and diagnoses, whereas interview data provided a better measure of illness, functional impairment and health in a broader sense. CONCLUSIONS: Both medical records and interviews yield good information of elderly people's health status, but they focus on different aspects of health.

Adult↗
PubMed1992

The chiropractic services market: a literature review.

This article surveys the economic literature on chiropractors. Chiropractors provide a substantial amount of care for those with various neuro-musculo-skeletal disorders and represent the fastest growing segment of the professional health services market. Yet the study of the profession has been neglected in the health services research literature. The goals of this article are to take stock of the existing literature and data sources. After providing background information, including recent developments in antitrust, I merge various data sources to assess the growth of expenditures for chiropractic care and the proportion of the population using this care. Other data sources and features are also described. I conclude with a discussion of the significance of further research on the profession to existing policy efforts to contain costs and improve health care delivery.

Chiropractic↗
PubMed1984

Church records as a source of data on Mexican migrant networks: a methodological note.

Marriage records from churches serving migrant communities are examined as a source of data on migration from Mexico to the United States. In particular, "this article discusses the methodological issues in the study of Mexican migration initiated by Cornelius and others.... It addresses two problems: the need to locate strategic regions in Mexico before field-work is begun; and the need to develop techniques for longitudinal studies of migration networks." The data used in the analysis are from the records of a church in Santa Ana, California, and cover the period 1947-1979.

Americas↗
PubMed1980

Use of Bernoulli census and log-linear methods for estimating the prevalence of spina bifida in livebirths and the completeness of vital record reports in New York State.

Data from birth certificates (BC), death certificates (DC) and medical rehabilitation files (MR) were analyzed to estimate the livebirth prevalence of spina bifida in upstate New York in 1969-1974 and the completeness of the data sources. Birth certificates listed about 68% of cases, death certificates about 27% and medical rehabilitation files about 25%. The three sources together, it is estimated, included only about 80% of cases in the population. For each source, comparisons of estimates of completeness derived using each of the other two as reference sources were found to be useful for evaluating the likelihood of source dependence. The estimated livebirth prevalence rate, adjusting for incomplete reporting and the observed negative dependence of MR and DC sources, was 0.85 per 1000 livebirths by both Bernoulli census and log-linear methods. Taking into account in addition evidence for a BC-DC positive dependence, the resulting prevalence rate estimates were slightly higher, 0.88 per 1000 by log-linear methods and 0.90 per 1000 by the Bernoulli census approach. In view of the likely BC-DC positive dependence, it is suggested that Bernoulli census estimates derived using only these two sources without some ancillary third data source are likely to be biased to a false low figure. Nevertheless, estimates from BC and DC alone may still be useful in establishing that the prevalence rate is above some minimum figure, for example a "breakeven" prevalence rate, in cost-benefit analyses of a possible prevention program.

Birth Certificates↗
PubMed2002

Surveillance of work-related disorders in Australia using general practitioner data.

OBJECTIVES: The focus of this paper is to compare the main findings regarding work-related problems managed in general practice with those of other data sources in the occupational and public health arenas that provide some information on work-related disorders in Australia, in order to examine the implications for surveillance and prevention. METHODS: Data on work-related disorders managed in general practice were obtained from a larger study of general practice activity that involved a cluster random sample of all significantly active general practitioners in Australia from 1998 to 2000. These data were compared with other Australian datasets containing information on work-related disorders. RESULTS: Despite a predominance of musculoskeletal conditions in all the data sources, general practitioner data provided a different picture of work-related disorders in the community to workers' compensation information from the National Data Set of Compensation-based Statistics (NDS) and the limited information on work-related disorders available from other studies of general practice and emergency departments. The mix of conditions was different in many aspects, and diseases were much less common in the NDS. CONCLUSIONS: General practitioner data supplement data provided by other sources, particularly the NDS, and make an important contribution to filling some of the gaps in information about work-related diseases and more minor work-related injuries. IMPLICATIONS: General practitioners could prove a useful supplementary source of data on work-related disorders, but the optimal content of, and method for obtaining, these data is not clear.

Accidents, Occupational↗
PubMed1995

The epidemiology of occupational contact dermatitis.

The dermatologist who is aware of the epidemiology of occupational contact dermatitis (OCD) can find this information helpful in making a diagnosis, determining etiology, and recommending preventive efforts. This article reviews some of the available epidemiologic data sources and their limitations. These data sources provide important information on the prevalence and incidence, the public health importance, the risk factors, the common etiologic agents, the prognosis, and the preventive measures for OCD.

Dermatitis, Occupational↗