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PubMed2004

Developing a comprehensive pesticide health effects tracking system for an urban setting: New York City's approach.

In recent years, there have been substantial investments and improvements in federal and state surveillance systems to track the health effects from pesticide exposure. These surveillance systems help to identify risk factors for occupational exposure to pesticides, patterns in poisonings, clusters of disease, and populations at risk of exposure from pesticide use. Data from pesticide use registries and recent epidemiologic evidence pointing to health risks from urban residential pesticide use make a strong case for understanding better the sale, application, and use of pesticides in cities. In this article, we describe plans for the development of a pesticide tracking system for New York City that will help to elucidate where and why pesticides are used, potential risks to varied populations, and the health consequences of their use. The results of an inventory of data sources are presented along with a description of their relevance to pesticide tracking. We also discuss practical, logistical, and methodologic difficulties of linking multiple secondary data sources with different levels of person, place, and time descriptors.

Data Collection↗
PubMed2006

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

BACKGROUND: Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task. RESULTS: In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project. The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses. Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access. CONCLUSION: JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in fruit exportation". However, due to its ability to organize and visualize data from external pipelines, JUICE is a flexible data management system that should be useful for other EST/Genome projects. The JUICE data management system is released under the Open Source GNU Lesser General Public License (LGPL). JUICE may be downloaded from http://genoma.unab.cl/juice_system/ or http://www.genomavegetal.cl/juice_system/.

Chromatography↗
PubMed1992

Accuracy and completeness of Scottish mental hospital in-patient data.

In Scotland the Information and Statistics Division of the Scottish Office Home and Health Department maintains a computerised record of patients who have been admitted to, discharged from or have died in Scottish mental hospitals. This data source is of particular value to those involved in planning health care provision and to epidemiologists. The present study assesses the quality of these data in relation to patients with verified presenile dementia who have been discharged from the Royal Edinburgh Hospital between 1974 and 1988. Seventeen per cent of presenile patients were not identified and 23% of patients were wrongly classified. More than 93% of patients with presenile Alzheimer's disease were identified, though often under a variety of other diagnostic codes. These findings highlight limitations of the data supplied and suggest that the usefulness of this enviable and unique data source could be enhanced if the medical profession took greater care in clearly stating an International Classification of Diseases diagnosis in a patient's hospital record.

Data Collection↗
PubMed2005

Predicting inhibitory drug-drug interactions and evaluating drug interaction reports using inhibition constants.

OBJECTIVE: To review the use of inhibitory constants (Ki) determined from in vitro experiments in the prediction of the significance of inhibitory drug-drug interactions (DDIs). DATA SOURCES: Searches of MEDLINE (1966-August 2004) and manual review of journals, conference proceedings, reference textbooks, and Web sites were performed using the key search terms cytochrome P450, drug-drug interaction, inhibition constant, and Ki. STUDY SELECTION AND DATA EXTRACTION: All articles identified from the data sources were evaluated, and information deemed relevant was included for this review. DATA SYNTHESIS: The cytochrome P450 isoenzymes factor prominently in the explanation of numerous DDIs. Although the regulation of these enzymes by one drug can affect the pharmacokinetics of other drugs, the consequences may not necessarily be significant either in terms of pharmacokinetic or clinical outcomes. Yet, many DDI monographs originate as unconfirmed case reports that implicate the influence of one drug on the CYP-mediated metabolism of another, and these often uncorroborated mechanisms can eventually become regarded as dogma. One consequence of this process is the over-prediction of potentially important DDIs. The pharmaceutical industry, Food and Drug Administration, and pharmaceutical scientists have developed a strategy for predicting the significance of inhibitory DDIs at the earliest possible stages of drug development based on a new chemical entity's Ki value, determined in vitro. CONCLUSIONS: We suggest that the use of Ki values of drugs purported to behave as CYP inhibitors be incorporated in the assessment of case reports that ascribe DDIs to inhibition of metabolism of one drug by another.

Area Under Curve↗
PubMed2004

An architecture for biological information extraction and representation.

MOTIVATIONS: Technological advances in biomedical research are generating a plethora of heterogeneous data at a high rate. There is a critical need for extraction, integration and management tools for information discovery and synthesis from these heterogeneous data. RESULTS: In this paper, we present a general architecture, called ALFA, for information extraction and representation from diverse biological data. The ALFA architecture consists of: (i) a networked, hierarchical, hyper-graph object model for representing information from heterogeneous data sources in a standardized, structured format; and (ii) a suite of integrated, interactive software tools for information extraction and representation from diverse biological data sources. As part of our research efforts to explore this space, we have currently prototyped the ALFA object model and a set of interactive software tools for searching, filtering, and extracting information from scientific text. In particular, we describe BioFerret, a meta-search tool for searching and filtering relevant information from the web, and ALFA Text Viewer, an interactive tool for user-guided extraction, disambiguation, and representation of information from scientific text. We further demonstrate the potential of our tools in integrating the extracted information with experimental data and diagrammatic biological models via the common underlying ALFA representation. CONTACT: aditya_vailaya@agilent.com.

Abstracting and Indexing↗
PubMed2004

Population pharmacokinetics II: estimation methods.

OBJECTIVE: To present, compare, and contrast the various approaches to estimating population pharmacokinetic (PPK) models with respect to the mathematical foundation, statistical aspects, software programs for implementation, and underlying assumptions. DATA SOURCES: Information on PPK was retrieved from a MEDLINE search (1977-August 2004) of literature and a bibliographic review of review articles and books. This information is used in conjunction with experience to explain the various methodologic approaches to PPK. STUDY SELECTION AND DATA EXTRACTION: All articles indentified from data sources were evaluated and relevant information was included in this review. DATA SYNTHESIS: Over 80 articles dealing with PPK estimation methods and/or their implementation were identified and reviewed. Sixty-four of these were chosen for their direct relevance to the subject of this article. Different estimation methods ranging from the naive averaging and naive pooled approaches through the standard two-stage approach to the nonlinear mixed-effects modeling approaches for estimating PPK are reviewed with their advantages and limitations. CONCLUSIONS: PPK estimation methods that rely on the characterizing of mixed (fixed and random) effects are known to produce PPK parameter estimates that are less biased than those obtained using the naive and standard two-stage approaches. The NONMEM software is the most widely used software for the characterization of PPK.

Bayes Theorem↗
PubMed2005

Computations of confidence intervals for estimates in the United States National Hospital Discharge Survey, 1979-2000.

INTRODUCTION: The National Hospital Discharge Survey is a primary data source for epidemiology research in the United States. To ensure that estimates are reliable, confidence intervals need to be calculated. The original survey data source is not available to the public, and the usual statistical methods are unsuitable for calculating confidence intervals. Instead, calculating confidence intervals requires using the statistical methods and relative standard errors that the U.S. National Center for Health Statistics has provided. However, the relative standard error parameters differ by hospital, patient category, and group. They also change yearly with sampling and are expressed differently before and during or after 1988. Consequently, manual computations of confidence intervals with multiple groups, diseases, and years are inefficient and prone to error. We developed a SAS program to compute confidence intervals for National Hospital Discharge Survey data from 1979 through 2000, newborns excluded. METHODS: We transposed 22 tables of relative standard error parameters (one for each year) into two new parameter tables that maintain the sampling designs before 1988 and during and after 1988 but are similar in overall structure. We unified all values to make each set of relative standard error parameters unique. We developed a program, COMPURSE, to search for relative standard error parameters for inputted estimates and to calculate confidence intervals. We set up an interface program for users to enter data, time period, confidence interval level, and output location; to read the relative standard error parameter tables; and to run the COMPURSE program. RESULTS: For different sets of National Hospital Discharge Survey data, COMPURSE efficiently and correctly retrieved relevant relative standard error parameters for estimates and accurately calculated relative standard errors, standard errors, and confidence intervals for annual estimates, multiple-year summaries, and average annual estimates. CONCLUSION: The program COMPURSE helps users analyze National Hospital Discharge Survey data efficiently.

Confidence Intervals↗
PubMed1995

Estimation of reference change limits using patient data.

Two approaches for deriving reference change limits from patient data are described. In the direct method, hospital database information is used for the selection of appropriate reference groups. If database information is not sufficient or reliable enough, but still most of the source data can be considered as health-related, an indirect method can be applied in the calculation of rough estimates for reference change limits. A computer program developed by us, GraphROC for Windows, includes both methods for the estimation of change limits from patient data. Time between specimen collections should be included as one classifying factor in the selection of source data. When only one previous result is available for comparison, change limits based on the reference sample group form the only available guide for clinical interpretation. However, when several previous results are available and the within-subject variances for the considered analyte are known to be heterogeneous between individuals, the clinical interpretation should rather be based on application of time series analysis.

Data Interpretation, Statistical↗
PubMed2004

The burden of complex genetics in brain disorders.

BACKGROUND: Few data estimate the impact of complex genetics in neuropsychiatric illness, making it likely that this impact could be underappreciated. OBJECTIVE: To provide estimates of the impact of complex genetics in neuropsychiatric disorders in the United States, based on estimates of disease costs to US society, disease heritability, and mendelian contributions to disease. DATA SOURCES, STUDY SELECTION, AND DATA EXTRACTION: Costs were estimated from literature sources and Lewin-National Foundation for Brain Research estimates updated for population growth and consumer price index inflation. Heritability estimates came from available twin data. Estimates of mendelian contributions came from the Online Mendelian Inheritance in Man database and our perspectives. CONCLUSIONS: Brain and nervous system disorders may cost the United States as much as US dollars 1.2 trillion annually, and affect many millions of Americans each year. Twin data suggest that more than 40% of the societal burden of brain disorders is likely to be genetically mediated. Most of this disease burden arises from complex multigene genetics as well as from environmental influences. The large sizes of these complex genetic burdens should encourage careful molecular and clinical work to link disease-vulnerability allelic variants with the pathogenesis, nosologic characteristics, prevention, diagnostics, and therapeutics of brain disorders.

Brain Diseases↗
PubMed2000

Periodontal disease in American Indians and Alaska Natives.

OBJECTIVE: The primary purpose of this paper is to provide information on the periodontal disease status of Native Americans using a variety of data sources. The impact of periodontal disease on the provision of dental care within the Indian Health Service (IHS) is also discussed. METHODS: Four data sources were used to evaluate the periodontal disease status of Native Americans: IHS periodontal disease monitoring system (1962-78), 1984 IHS Patient Oral Health Survey, 1990 WHO community-based survey (ICS-II), and the 1991 IHS Patient Oral Health Survey. RESULTS: There appears to be a trend toward a higher prevalence of incipient and overt periodontal disease among Native Americans over time. The prevalence of overt periodontal disease (periodontal pockets > 5.5 mm) is higher among Native American diabetic patients than nondiabetic patients (34% vs 19%). CONCLUSIONS: Due to the variety of indices used by the IHS during the last 20 years, it is difficult to make direct comparisons of the available periodontal disease data. However, it appears that the prevalence of periodontal disease among Native Americans is increasing. Type II diabetes accounts for significant increases in periodontal disease and tooth loss in Native American populations. Certain forms of early onset periodontal disease also may pose significant threats to the oral health of Native Americans.

Adult↗
PubMed1998

Neuropharmacology of St. John's Wort (Hypericum).

OBJECTIVE: To review preclinical information related to possible antidepressant mechanism(s) of action of St. John's wort in order to address the issue of whether its purported clinical effectiveness has a rational pharmacologic basis. DATA SOURCES: Primary and review articles were identified by a MEDLINE search (1966-January 1998) and through secondary sources. Many of the original German articles had English abstracts, but where necessary, German articles were translated into English. The results of a new screen of hypericin activity at receptor and uptake sites are summarized. STUDY SELECTION AND DATA EXTRACTION: All of the articles identified from the data sources were evaluated and all information deemed relevant was included in this review. DATA SYNTHESIS: The neuropharmacology of St. John's wort has been examined in only a few studies. A mechanism similar to that of the synthetic antidepressants, such as the selective serotonin-reuptake inhibitors or monoamine oxidase (MAO) inhibitors, might play a role, but other mechanisms are possible. CONCLUSIONS: Hypericum extracts have only weak activity in assays related to mechanisms of the synthetic antidepressants, that is, inhibition of MAO, catechol O-methyltransferase, or serotonin reuptake. It has been postulated that the clinical efficacy of St. John's wort could be attributable to the combined contribution of several mechanisms, each one too weak by itself to account for the overall effect. The recent demonstration of a significant affinity of hypericin for sigma receptors presents new possibilities for consideration.

Animals↗
PubMed2003

What can we learn about asthma from studying occupational asthma?

OBJECTIVE: To review the clinical features and underlying mechanisms of occupational asthma in an attempt to glean insights into various other forms of asthma. DATA SOURCES: Published literature, including consensus guidelines on diagnosis and management of occupational asthma. STUDY SELECTION: This article represents a synthesis of these data sources and the opinion of the author. RESULTS: Occupational asthma may be caused by a variety of mechanisms, including both IgE-dependent and non-IgE-dependent immunological processes. IgE-dependent mechanisms are responsible for reactions to all high-molecular-weight occupational antigens and to some but not all low-molecular-weight antigens. Factors in sensitization and onset include the general genetic predisposition to make IgE and the specific responsiveness of the individual to particular allergens. Once sensitized, the main factor that influences the onset of symptoms is the degree of exposure. In general, the higher the level of exposure, the more likely the sensitized person is to develop asthma. CONCLUSIONS: Occupational asthma can be induced by a variety of agents that appear to use different mechanisms to affect the airway. Studies of the remission of occupational asthma indicate that resolution is a slow process. However, the study of occupational asthma may eventually allow us to identify treatments that will accelerate remission or induce remission in other forms of asthma.

Allergens↗
PubMed2001

The rational clinical examination. Does this patient have a torn meniscus or ligament of the knee? Value of the physical examination.

CONTEXT: While most meniscal or ligamentous knee injuries heal with nonoperative treatments, a subset should be treated with arthroscopic or open surgery. OBJECTIVE: To analyze the accuracy of the clinical examination for meniscal or ligamentous knee injuries. DATA SOURCES: MEDLINE (1966-December 31, 2000) and HealthSTAR (1975-December 31, 2000) databases were searched for English-language articles describing the diagnostic accuracy of individual examination items for the knee and a combination of physical examination items (composite examination). Other data sources included reference lists from relevant articles. STUDY SELECTION: Studies selected for data extraction were those that compared the performance of the physical examination of the knee with a reference standard, such as arthroscopy, arthrotomy, or magnetic resonance imaging. Eighty-eight articles were identified, of which 23 (26%) met inclusion criteria. DATA EXTRACTION: A rheumatologist and an orthopedic surgeon independently reviewed each article using a standardized rating scale that scored the assembly of the study, the relevance of the patients enrolled, the appropriateness of the reference standard, and the blinding of the examiner. DATA SYNTHESIS: Summary likelihood ratios (LRs) were estimated from random effects models. The summary LRs for physical examination for tears of the anterior cruciate ligament, using the anterior drawer test, were 3.8 (95% confidence interval [CI], 0.7-22.0) for a positive examination and 0.30 (95% CI, 0.05-1.50) for a negative examination; the Lachman test, 25.0 (95% CI, 2.7-651.0) and 0.1 (95% CI, 0.0-0.4); and the composite assessment, 25.0 (95% CI, 2.1-306.0) and 0.04 (95% CI, 0.01-0.48), respectively. The LRs could not be generated for any specific examination maneuver for a posterior cruciate ligament tear, but the composite assessment had an LR of 21.0 (95% CI, 2.1-205.0) for a positive examination and 0.05 (95% CI, 0.01-0.50) for a negative examination. Determination of meniscal lesions, using McMurray test, had an LR of 1.3 (95% CI, 0.9-1.7) for a positive examination and 0.8 (95% CI, 0.6-1.1) for a negative examination; joint line tenderness, 0.9 (95% CI, 0.8-1.0) and 1.1 (95% CI, 1.0-1.3); and the composite assessment, 2.7 (95% CI, 1.4-5.1) and 0.4 (95% CI, 0.2-0.7), respectively. CONCLUSION: The composite examination for specific meniscal or ligamentous injuries of the knee performed much better than specific maneuvers, suggesting that synthesis of a group of examination maneuvers and historical items may be required for adequate diagnosis.

Anterior Cruciate Ligament Injuries↗
PubMed2004

High- versus low-dose oxytocin for augmentation or induction of labor.

OBJECTIVE: To compare the use of high- and low-dose oxytocin for augmentation or induction of labor. DATA SOURCES: Clinical trials were accessed through MEDLINE (1966-November 2003). Published literature relevant to the use of oxytocin for augmentation or induction of labor was evaluated. STUDY SELECTION AND DATA EXTRACTION: Articles identified from the data sources were evaluated and included if they were clinical trials comparing high-versus low-dose oxytocin for augmentation or induction of labor. DATA SYNTHESIS: Oxytocin is a treatment of choice for augmentation and induction of labor; however, no consensus exists regarding optimal dosing. Relevant studies comparing high-dose (2-6 mU/min) and low-dose (1-2 mU/min) therapy for labor augmentation and induction were evaluated. CONCLUSIONS: High-dose oxytocin decreases the time from admission to vaginal delivery, but does not appear to decrease the incidence of cesarean sections when compared with low-dose therapy.

Cesarean Section↗
PubMed2003

Analgesic efficacy of calcitonin for vertebral fracture pain.

OBJECTIVE: To evaluate the analgesic efficacy of calcitonin for treating the pain of vertebral fractures associated with osteoporosis. DATA SOURCES: Searches of MEDLINE (1966-July 2002), Cochrane Library, International Pharmaceutical Abstracts (1977-July 2002), and an extensive manual review of journals were performed using the key search terms calcitonin, analgesic, osteoporosis, vertebral fracture, and pain. STUDY SELECTION AND DATA EXTRACTION: All articles identified from the data sources were evaluated and all information deemed relevant was included for this review. DATA SYNTHESIS: Fractures, especially vertebral fractures, are a common complication of osteoporosis, leading to significant pain. Calcitonin has been studied for its analgesic properties. Fourteen double-blind, placebo-controlled trials that evaluated the analgesic efficacy of calcitonin for osteoporosis-related vertebral fracture pain were identified and reviewed. Thirteen of these studies demonstrated statistically significant improvement in pain or function in calcitonin-treated patients. CONCLUSIONS: Calcitonin has proven efficacy in acute pain associated with osteoporosis-related vertebral fractures. Analgesic effects are seen with intranasal, parenteral, and rectal administration. Future studies comparing calcitonin with other commonly used analgesics are needed to more clearly define its place in therapy.

Analgesics↗
PubMed2003

Efficacy of stimulants in adult ADHD.

OBJECTIVE: To review the literature regarding the efficacy of stimulants to treat attention-deficit-hyperactivity disorder (ADHD) in adults. DATA SOURCES: The relevant pharmaceutical manufacturers were contacted, and searches of MEDLINE (1966-December 2002) and the reference sections of each article obtained were performed using the key search terms: adult ADHD, stimulants, methylphenidate, amphetamines, and pemoline. STUDY SELECTION AND DATA EXTRACTION: All English-language original studies identified from the data sources were evaluated and all information deemed relevant was included in the review. DATA SYNTHESIS: Studies involving methylphenidate, amphetamines, and pemoline were identified. There was evidence for the efficacy of amphetamines from 5 studies (4 controlled, 1 open). Methylphenidate data from 6 controlled trials were conflicting. Three studies indicated efficacy; 2 studies failed to show efficacy, possibly due to methodologic reasons; and the results from 1 study were conflicting. The limited data from 1 controlled and 1 open study indicated that pemoline may be less effective than methylphenidate and amphetamines. CONCLUSIONS: While the current limited data indicate that stimulants may be effective in adult ADHD, more data are required to confirm long-term efficacy.

Adult↗
PubMed2001

Antimicrobial-coated/bonded and -impregnated intravascular catheters.

OBJECTIVE: To review the literature regarding the prevention of catheter colonization and catheter-related bloodstream infections (CRBIs) with the use of antimicrobial-coated/bonded and -impregnated intravascular catheters. DATA SOURCES: Primary and review English-language literature were identified using MEDLINE (1966-September 2000) pertaining to the key terms antibiotic, antimicrobial, antiseptic, silver, and bonded, coated, Impregnated catheters. In addition, textbooks and relevant reference lists were reviewed. DATA EXTRACTION: All articles identified through the data sources were evaluated. Information deemed relevant to the objectives of the review was included. DATA SYNTHESIS: Significant morbidity and mortality are associated with the development of CRBIs. Preventative measures such as modification of these catheters with antimicrobial coating/bonding have produced varying results. Trials evaluating cefazolin, teicoplanin, vancomycin, silver, and chlorhexidine-silver sulfadiazine (C-SS) used for coated/bonded intravascular catheters have not demonstrated a consistent decrease in the incidence of CRBIs. However, a meta-analysis of trials evaluating C-SS intravascular catheters demonstrated a statistically significant reduction in CRBIs. A larger reduction in CRBIs has been reported with minocycline-rifampin (M-R) versus C-SS intravascular catheters. Use of the M-R and C-SS catheters may result in a cost savings of $100 million and reduce as many as 12,000 CRBI-related deaths annually when used short term (<7 d). CONCLUSIONS: When used for short-term catheterization, M-R catheters appear to be superior to the currently available C-SS catheters at preventing CRBIs. Significant cost savings and reduction in mortality can be anticipated with the use of M-R catheters.

Adult↗
PubMed1998

Seniors' needs for health-related personal assistance.

OBJECTIVES: This article examines social and economic differences in the prevalence of needs and unmet needs for health-related personal assistance among the household population aged 65 and older and the sources from which they received support. DATA SOURCE: The data are from the 1991 Health and Activity Limitation Survey (HALS). ANALYTICAL TECHNIQUES: All calculations were based on weighted data. Age-standardized percentages of people with needs and unmet needs for personal assistance were calculated by sex, marital status, living arrangements, education, and household income. MAIN RESULTS: In 1991, 30% of seniors living in private households had some need for health-related personal assistance. Three-quarters of them required help only with instrumental activities of daily living (IADL); the remainder needed help with basic activities of daily living (ADL). The prevalence of need and unmet need was higher among women than men, was inversely related to household income and education, and was relatively high among formerly married seniors and those living alone. Household seniors were more likely to receive personal assistance from informal than formal sources, although this varied depending on their socioeconomic characteristics and the type of assistance they received.

Activities of Daily Living↗