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PubMed1995

Converting a legacy system database into relational format to enhance query efficiency.

The analysis of clinical data collected over time can provide important insight into the health care process. Unfortunately, much of the electronic clinical data that exists today is stored in legacy systems, making it difficult to access and share the information. An approach is needed to improve the accessibility of electronic data stored in legacy system databases. In this study, a legacy database is converted into a relational format in the personal computer environment. The impact of such a conversion on query performance is evaluated, and issues that need to be considered when converting a legacy system database are identified.

Computer Systems↗

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↗

PubMed2005

[Watercourses protection and urban planning].

The work analyses the complex relationships that link urban planning and environmental protection referring, in particular, to watercourses defence. The close interactions existing between development of human activities on territory and the hydrological cycle point out the necessity of a watershed-scale planning. This regional planning, in fact, allows both problems of protection and optimal use of hydrological resources in terms not only of punctual actions, but also of land use. In this context, the fundamental roles played by geographical and environmental information systems are shown and analysed with special regard to their importance in fostering citizens participation in decisional processes by means of an easier access to environmental data and information available to public authorities.

Access to Information↗

PubMed2000

Tacrine for Alzheimer's disease.

BACKGROUND: Tacrine is one of the first drugs to be widely marketed for the loss of memory and intellectual decline in Alzheimer's disease. The alleged success of tacrine in the treatment of these symptoms has been heralded as confirmation of the cholinergic theory of Alzheimer's disease. However, the efficacy of tacrine for symptoms of dementia remains controversial. This is reflected by the low rate of prescription of tacrine in countries where it is approved and the lack of approval by several regulatory authorities in Europe and elsewhere. The uncertainty about the efficacy of tacrine is due to the difficulties in interpretation of the results from the clinical trials. The reasons for this are the small effects of tacrine compared to placebo for all outcomes; the high incidence of adverse events; the lack of benefit observed in several trials; the use of cross-over designs and their associated methodological problems in a disease like dementia; the use of different measurement scales to assess outcome in different trials; and the problem of high dropout rates. OBJECTIVES: To determine the clinical efficacy of tacrine for the symptoms of Alzheimer's disease. SEARCH STRATEGY: The Cochrane Dementia Group Register of Clinical Trials was searched using the terms 'tacrine', 'tetrahydroaminoacridine' and 'THA' (see the Group's search strategy for full details). SELECTION CRITERIA: All unconfounded, double-blind, randomized trials in which treatment with tacrine was administered for more than a day and compared to placebo in patients with dementia of the Alzheimer's type. DATA COLLECTION AND ANALYSIS: Data were extracted independently by two reviewers, pooled if appropriate and possible, and the pooled odds ratios (95%CI) or the average differences (95%CI) were estimated. Where possible, intention-to-treat data were used. MAIN RESULTS: This review produced no clear results. The results were compatible with tacrine producing improvement, no change or even harm for those with Alzheimer's disease. It was not possible to use many of the published results in a combined analysis. For measures of overall clinical improvement, the intention-to-treat analyses failed to detect any difference between tacrine and placebo (OR 0.87; 95%CI 0.61 - 1.23). Behavioural disturbance, as measured by the Alzheimer's Disease Assessment Scale-noncognitive, failed to detect any difference between tacrine and placebo (SMD -0.04; 95%CI -0.52 - 0.43). For cognition function, the effect of tacrine was not statistically significantly different from placebo for the MiniMental State Examination score (0-30; high =good) (SMD 0.14; 95%CI -0.02 - 0.30) and was barely statistically significantly in favour of treatment for the Alzheimer's Disease Assessment Scale-cognitive scale (SMD -0.22; 95%CI -0.32 - -0.13). Adverse events were not reported in a systematic way in the different trials, making formal comparison difficult. Raised serum liver enzymes was the major reason for withdrawal. The odds ratio for withdrawal due to an adverse event was significantly different from one, the control group experienced fewer events (OR 5.7; 95%CI 4.1-7.9). Gastrointestinal side effects (diarrhoea, anorexia, dyspepsia and abdominal pain) were the other major cause of adverse events and for withdrawal, and the odds ratio for withdrawal was also significantly different from one in favour of the control group (OR 3.8; 95%CI 2.8-5.1). No deaths were reported in any of the studies during the trial period, up to six months. REVIEWER'S CONCLUSIONS: This review provides no convincing evidence that tacrine is a useful treatment for the symptoms of Alzheimer's disease. However, as so few trials presented data in a format suitable for pooling, the results of this review may be modified when further data from all relevant trials are included. There is an urgent need for the independent evaluation of the data already existing in the trials but not accessible through published or grouped data. A

Alzheimer Disease↗

PubMedDate not supplied

Reweighting DHS data to serve multiple perspectives.

Information about health and family planning infrastructures is collected through the service availability module (SAM), an important feature of the Demographic and Health Surveys (DHS) conducted in many developing countries. The DHS samples were designed to provide a representative sample of households and women of reproductive age. Using the weights routinely provided with DHS data sets, service accessibility can be described straightforwardly at the individual and household levels. However, without further adjustment, SAM data do not provide a representative picture of service delivery at the community, or primary sampling unit, level, where the data are collected. This report proposes a methodology for reweighting the SAM data, using rural data from the Egypt DHS as an illustration, so that available family planning facilities at this level may be usefully characterized at little additional cost.

Adolescent↗

PubMed2006

Using information from public Arabidopsis databases to aid research.

The volume of Arabidopsis information has increased enormously in recent years as a result of the sequencing of the genome and other large-scale genomic projects. Much of the data are stored in public databases, where data are organized, analyzed, and made freely accessible to the research community. These databases are resources that researchers can utilize for making predictions and developing testable hypotheses. The methods in this chapter describe ways to access and utilize Arabidopsis data and genomic resources found in databases.

Access to Information↗

PubMed1995

National Patient Master Index in Singapore.

It has been the practice of hospitals and medical institutions to keep their patients' medical records. Access to such valuable information will be confined within the respective health institutions if there is no proper infrastructure to facilitate sharing of the information. On the other hand, it has been the wish of medical professionals, as well as patients who frequent hospitals and medical institutions that patients' medical records, especially essential medical conditions, are readily available, whenever required, regardless of the health institution by which the patient is being attended to. In response, the National Patient Master Index (NPMI) system was conceived and implemented by the Singapore Ministry of Health in 1994. The NPMI system aims at providing a patient database at national level that allows authorised users faster access to a patient's essential medical data thereby facilitating patient management. This paper describes the implementation of the NPMI system, its data elements, system functionality and access control to address data confidentiality and privacy.

Computer Security↗

PubMed1999

Problems in the design and reporting of trials of antifungal agents encountered during meta-analysis.

Meta-analyses may become biased if the reported data in the individual trials are biased and if overlap among trials cannot be identified. We describe the unanticipated problems we encountered in collecting data for a meta-analysis comparing a new antifungal agent, fluconazole, with amphotericin B in patients with cancer complicated by neutropenia. In 3 large trials that comprised 43% of the patients identified for the meta-analysis, results for amphotericin B were combined with results for nystatin in a "polyene" group. Because nystatin is recognized as an ineffective drug in these circumstances, this approach creates a bias in favor of fluconazole. Furthermore, 79% of the patients were randomized to receive oral amphotericin B, which is poorly absorbed and not an established treatment, in contrast to intravenous amphotericin B, which was administered in 4 of 5 placebo-controlled trials, or 86% of patients. It was unclear whether there was overlap among the "polyene" trials, and it is possible that results from single-center trials were included in multicenter trial reports. We were unable to obtain information to clarify these issues from the trial authors or the manufacturer of fluconazole. Two of 11 responding authors replied that the data were with the drug manufacturer and two indicated that they did not have access to their data because of change of affiliation. In the meta-analyses, fluconazole and amphotericin B (mostly given orally) had similar effects (13 trials), whereas nystatin was no better than placebo (3 trials). Since individual trials are rarely conclusive, investigators, institutions, and pharmaceutical companies should provide essential details about their work to ensure that meta-analyses can accurately reflect the studies conducted and that patients will realize maximum benefits from treatments. We recommend that investigators keep copies of their trial data to help facilitate accurate and unbiased meta-analyses.

Amphotericin B↗

PubMed2005

Grid-based dynamic electronic publication: a case study using combined experiment and simulation studies of crown ethers at the air/water interface.

Conventional paper-based scientific publications are limited in the amount of data and interaction they can provide. Simply placing an electronic copy of such a publication on the web makes for easier distribution, but more can be achieved by making use of the technology to navigate through the paper, to show the links between calculated parameters and the data, and provide access to the chain of calculated results all the way back to the raw data and ultimately the laboratory notebook. While the paper version of this publication is in a relatively conventional form, an interactive demonstrator version (available at http://epaper.combe.chem.soton.ac.uk and as an installable package) illustrates the concepts of publication@source, whereby all the figures and data presented in the paper are linked back to the original raw data together with a description of the processes by which the raw data were analysed. This level of interactivity is achieved using semantic technologies, which have the additional advantage of making the final document subsequently available and navigable by automated techniques. We present the combined information from experimental studies of surface tension and second harmonic generation (SHG) on the behaviour of benzo-15-crown-5 at the solution/air interface, together with a molecular dynamics computer simulation, to demonstrate how the simulation aids the interpretation of the SHG experiment. The adsorption isotherm was determined using SHG and fitted to a Langmuir isotherm giving Delta ads G0=26 kJ mol-1.

Air↗

PubMed2005

Smoking reduction does work: resulting alterations in the incidence and histological subtypes of lung cancer in New South Wales in the last 20 years.

BACKGROUND: There is irrefutable evidence of the association between lung cancer and smoking. The effects of public health campaigns to reduce population-smoking rates on the incidence and the histological distribution of lung cancer were examined. METHODS: The data held in the New South Wales Cancer Registry from 1972 to 2001 was accessed. RESULTS: The data revealed a decreasing incidence of lung cancer amongst males and a rate that continued to increase amongst females. Interestingly, there was also an effect on the histological distribution of lung cancers, with falling rates of small cell lung cancer and squamous cell cancer, both of which have a high association with smoking; and an increasing incidence of adenocarcinomas. CONCLUSIONS: These trends reveal patterns seen worldwide. The increasing proportion of adenocarcinomas in particular may be related to the changing composition of cigarettes and filters.

Carcinoma, Small Cell↗

PubMed2000

PhysioBank, PhysioToolkit, and PhysioNet: components of a new research resource for complex physiologic signals.

The newly inaugurated Research Resource for Complex Physiologic Signals, which was created under the auspices of the National Center for Research Resources of the National Institutes of Health, is intended to stimulate current research and new investigations in the study of cardiovascular and other complex biomedical signals. The resource has 3 interdependent components. PhysioBank is a large and growing archive of well-characterized digital recordings of physiological signals and related data for use by the biomedical research community. It currently includes databases of multiparameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and from patients with a variety of conditions with major public health implications, including life-threatening arrhythmias, congestive heart failure, sleep apnea, neurological disorders, and aging. PhysioToolkit is a library of open-source software for physiological signal processing and analysis, the detection of physiologically significant events using both classic techniques and novel methods based on statistical physics and nonlinear dynamics, the interactive display and characterization of signals, the creation of new databases, the simulation of physiological and other signals, the quantitative evaluation and comparison of analysis methods, and the analysis of nonstationary processes. PhysioNet is an on-line forum for the dissemination and exchange of recorded biomedical signals and open-source software for analyzing them. It provides facilities for the cooperative analysis of data and the evaluation of proposed new algorithms. In addition to providing free electronic access to PhysioBank data and PhysioToolkit software via the World Wide Web (http://www.physionet. org), PhysioNet offers services and training via on-line tutorials to assist users with varying levels of expertise.

Databases as Topic↗

PubMed2006

On the way to understand biological complexity in plants: S-nutrition as a case study for systems biology.

The establishment of technologies for high-throughput DNA sequencing (genomics), gene expression (transcriptomics), metabolite and ion analysis (metabolomics/ionomics) and protein analysis (proteomics) carries with it the challenge of processing and interpreting the accumulating data sets. Publicly accessible databases and newly development and adapted bioinformatic tools are employed to mine this data in order to filter relevant correlations and create models describing physiological states. These data allow the reconstruction of networks of interactions of the various cellular components as enzyme activities and complexes, gene expression, metabolite pools or pathway flux modes. Especially when merging information from transcriptomics, metabolomics and proteomics into consistent models, it will be possible to describe and predict the behaviour of biological systems, for example with respect to endogenous or environmental changes. However, to capture the interactions of network elements requires measurements under a variety of conditions to generate or refine existing models. The ultimate goal of systems biology is to understand the molecular principles governing plant responses and consistently explain plant physiology.

Arabidopsis↗

PubMed2003

Summary health statistics for U.S. children: National Health Interview Survey, 2000.

OBJECTIVES: This report presents statistics from the 2000 National Health Interview Survey on selected health measures for children under 18 years of age, classified by sex, age, race, Hispanic origin, family structure, parent's education, family income, poverty status, health insurance coverage, residence, region, and health status. The topics covered are asthma, allergies, learning disability, Attention Deficit Hyperactivity Disorder (ADHD), prescription medication, respondent-assessed health status, school-loss days, usual place of health care, time since last contact with a health care professional, unmet dental need, time since last dental contact, and selected measures of health care access. SOURCE OF DATA: The NHIS is a multistage probability sample survey conducted annually by interviewers of the U.S. Census Bureau for the National Center for Health Statistics, Centers for Disease Control and Prevention, and is representative of the civilian noninstitutionalized population of the United States. Data are collected during face-to-face interviews with adults present at the interview. Information about children is collected for one randomly selected child per family in face-to-face interviews with an adult proxy respondent familiar with the child's health. SELECTED HIGHLIGHTS: In 2000 most U.S. children under 18 years of age enjoyed excellent or very good health (83%). However, 12% had no health insurance coverage, and 6% had no usual place of health care. Twelve percent of children had ever been diagnosed with asthma. Eight percent of children 3-17 years of age had a learning disability, and 7% of children in this age group had ADHD. Lastly, 11% of children in single-mother families had two or more visits to an emergency room in the past year compared with 6% in two-parent families.

Absenteeism↗

PubMed2003

Summary health statistics for U.S. children: National Health Interview Survey, 2001.

OBJECTIVES: This report presents statistics from the 2001 National Health Interview Survey (NHIS) on selected health measures for children under 18 years of age, classified by sex, age, race, Hispanic origin, family structure, parent's education, family income, poverty status, health insurance coverage, residence, region, and health status. The topics covered are asthma, allergies, learning disability, Attention Deficit Hyperactivity Disorder (ADHD), prescription medication, respondent-assessed health status, school-loss days, usual place of health care, time since last contact with a health care professional, unmet dental need, time since last dental contact, and selected measures of health care access. SOURCE OF DATA: The NHIS is a multistage probability sample survey conducted annually by interviewers of the U.S. Census Bureau for the Centers for Disease Control and Prevention, National Center for Health Statistics, and is representative of the civilian noninstitutionalized population of the United States. Data are collected during face-to-face interviews with adults present at the interview. Information about children is collected for one randomly selected child per family in face-to-face interviews with an adult proxy respondent familiar with the child's health. SELECTED HIGHLIGHTS: In 2001, most U.S. children under 18 years of age enjoyed excellent or very good health (84%). However, 10% had no health insurance coverage, and 5% had no usual place of health care. Thirteen percent of children had ever been diagnosed with asthma. Eight percent of children 3-17 years of age had a learning disability, and 6% of children had ADHD. Lastly, 11% of children in single-mother families had two or more visits to an emergency room in the past year compared with 6% of children in two-parent families.

Adolescent↗

PubMedDate not supplied

MATCH: a maternal and child health information network.

The Maternal and Child Health Information Network--MATCH--was begun in 1984 as a demonstration project with support from the Division of Maternal and Child Health of the Health Resources and Services Administration, Public Health Service. The primary purpose of the project was the development of a system to manage data related to prenatal, child health, family planning, and genetic services that are delivered with State support in clinics in the State of Ohio. The design of MATCH enables the same data base to be used at both the State and local levels. Because it allows all participants, central and district, to manipulate the raw data, it is called an end-user--as opposed to a batch retrieval--system. Data recorded on individual forms during each client's visit to local service clinics are collected and entered into a microcomputer whose software package is a commercial data base. The clinic can then use the data for its purposes: program planning, management, evaluation, client referrals, appointment followup, quality control, and billing. The same data are also uploaded by central office staff to the State's DEC mainframe from data-filled disks mailed in by the clinics. Personnel who staff local projects can access their own data on the mainframe computer to generate reports for local use and send and receive messages electronically. That is, the system is "interactive." The intent is to first link data generated by the primary care and preventive programs of maternal and child health (MCH) in an information system,then link that system to other health data arriving at the State health department (for example, birth and death certificates), and, finally, to use the system as the basis for a State level MCH primary care data system in Ohio for surveillance, planning,management, quality control, accountability,and research purposes.

Child Health Services↗

PubMed1973

CAN-SDI: experience with multi-source computer based current awareness services in the National Science Library, Ottawa.

CAN/SDI is Canada's national Selective Dissemination of Information Service offering a choice of nine data bases to its scientific and technical community. The system is based on central processing at the National Science Library combined with the utilization of decentralized expertise and resources for profile formulation and user education. Its greatest strength lies in its wide interdisciplinary quality. The major advantage of centralized processing of many data bases is that Canadians need learn only one method of profile formulation to access many files. A breakdown of services used confirms that a single tape service does not cover all the information requirements of most users. On the average each profile accesses approximately 1.5 data bases. Constant subscriber growth and a low cancellation rate indicate that CAN/SDI is and will continue to be an important element in Canada's information system.

Canada↗

PubMed1994

Report on the clinical workstation and clinical data repository utilization at UNC Hospitals.

On December 1, 1993, we implemented version 2.1 of the Clinical Workstation-Clinical Data Repository application in the Ambulatory Care Center. This version of the workstation allowed access of laboratory data from the clinical data repository that had been populated by a real-time HL7 interface between the Clinical Data Repository and the Laboratory Information System. This implementation completed a major part of the Clinical Workstation project. Also in December, we implemented a security system that records the date and time, user logon code, clinical workstation functions used, and the patient medical record number on whom data were displayed. In addition to the security function, this system has proven to be a valuable tool in evaluating the utilization of the clinical workstation and is the source of the data presented in this paper.

Clinical Laboratory Information Systems↗

PubMed2002

SWEET-DB: an attempt to create annotated data collections for carbohydrates.

Complex carbohydrates are known as mediators of complex cellular events. Concerning their structural diversity, their potential of information content is several orders of magnitude higher in a short sequence than any other biological macromolecule. SWEET-DB (http://www.dkfz.de/spec2/sweetdb/) is an attempt to use modern web techniques to annotate and/or cross-reference carbohydrate-related data collections which allow glycoscientists to find important data for compounds of interest in a compact and well-structured representation. Currently, reference data taken from three data sources can be retrieved for a given carbohydrate (sub)structure. The sources are CarbBank structures and literature references (linked to NCBI PubMed service), NMR data taken from SugaBase and 3D co-ordinates generated with SWEET-II. The main purpose of SWEET-DB is to enable an easy access to all data stored for one carbohydrate structure entering a complete sequence or parts thereof. Access to SWEET-DB contents is provided with the help of separate input spreadsheets for (sub)structures, bibliographic data, general structural data like molecular weight, NMR spectra and biological data. A detailed online tutorial is available at http://www.dkfz.de/spec2/sweetdb/nar/.

Carbohydrate Conformation↗