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At least 307 records · Page 17Linked to original sources
PubMed1991

Estimating kappa from binocular data.

A common error in statistical analysis of ophthalmic data is the lack of accounting for the positive correlation generally present between observations made in fellow eyes. The alternative of data analysis from only one eye in each patient may lead to loss of power and unrealistically large confidence intervals. This paper discusses a method to estimate kappa, a measure of agreement between two graders, when both graders rate the same set of pairs of eyes. The method assumes that the true left-eye and right-eye kappa values are equal and makes use of the correlated binocular data to estimate confidence intervals for the common kappa. Simulations show that the new estimators are better than the estimator based on only one eye; new confidence intervals had the correct coverage probability, but were usually only about 70 per cent as wide as single-eye intervals. The general methodology described here applies to analysis of grader agreement in rating other paired body structures.

Atrophy↗
PubMed2000

Measuring our nation's diversity: developing a common language for data on race/ethnicity.

During the 4-year period 1993 through 1997, the Office of Management and Budget (OMB) undertook a comprehensive review of the statistical standards that are used throughout the federal government to gather and publish data on race and ethnicity. The primary objective of this review was to ensure that our standards provide a common language that reflects the increasing diversity of the US population and maintains our ability to monitor compliance with civil rights laws. The review culminated with the October 1997 issuance of OMB's "Standards for Maintaining, Collecting, and Presenting Federal Data on Race and Ethnicity." In this article, we describe key aspects of the process that was undertaken to review and revise the 1977 standards. We also attempt to dispel some myths and misunderstandings that have been associated with these standards.

Censuses↗
PubMed2003

Modelling the random effects covariance matrix in longitudinal data.

A common class of models for longitudinal data are random effects (mixed) models. In these models, the random effects covariance matrix is typically assumed constant across subject. However, in many situations this matrix may differ by measured covariates. In this paper, we propose an approach to model the random effects covariance matrix by using a special Cholesky decomposition of the matrix. In particular, we will allow the parameters that result from this decomposition to depend on subject-specific covariates and also explore ways to parsimoniously model these parameters. An advantage of this parameterization is that there is no concern about the positive definiteness of the resulting estimator of the covariance matrix. In addition, the parameters resulting from this decomposition have a sensible interpretation. We propose fully Bayesian modelling for which a simple Gibbs sampler can be implemented to sample from the posterior distribution of the parameters. We illustrate these models on data from depression studies and examine the impact of heterogeneity in the covariance matrix on estimation of both fixed and random effects.

Antidepressive Agents↗
PubMed2000

Accessing and distributing EMBL data using CORBA (common object request broker architecture).

BACKGROUND: The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. RESULTS: A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. CONCLUSIONS: The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems.

Computational Biology↗
PubMedDate not supplied

Tools for community-oriented primary care: a process for linking practice and community data.

BACKGROUND: Community-oriented primary care (COPC) is an increasingly attractive paradigm for primary care delivery. Further work is needed, however, to implement COPC in busy practice settings. This study reports a feasible method for linking practice and community health data for use in COPC. METHODS: Using one practice and its community as an example of the process, we sought data related to five common cancers. Data from readily accessible community sources were combined with practice morbidity data using commonly available computer hardware and software. RESULTS: We developed a user-friendly database and maps showing rates and distribution of the example diseases. We also developed strategies to obtain complete case identification and to address confidentiality and proprietary concerns. CONCLUSIONS: Understanding patterns of disease expression in the practice and the community is critical to the COPC process. Rapid, inexpensive methods for displaying these patterns, such as the database and maps described, must be accessible to clinicians if COPC is to move from theory into practice. Partnerships between health care providers and institutions can also help get this capability into the hands of clinicians.

Community Health Services↗
PubMed2002

Types of inter-atomic interactions at the MHC-peptide interface: identifying commonality from accumulated data.

BACKGROUND: Quantitative information on the types of inter-atomic interactions at the MHC-peptide interface will provide insights to backbone/sidechain atom preference during binding. Qualitative descriptions of such interactions in each complex have been documented by protein crystallographers. However, no comprehensive report is available to account for the common types of inter-atomic interactions in a set of MHC-peptide complexes characterized by variation in MHC allele and peptide sequence. The available x-ray crystallography data for these complexes in the Protein Databank (PDB) provides an opportunity to identify the prevalent types of such interactions at the binding interface. RESULTS: We calculated the percentage distributions of four types of interactions at varying inter-atomic distances. The mean percentage distribution for these interactions and their standard deviation about the mean distribution is presented. The prevalence of SS and SB interactions at the MHC-peptide interface is shown in this study. SB is clearly dominant at an inter-atomic distance of 3A. CONCLUSION: The prevalently dominant SB interactions at the interface suggest the importance of peptide backbone conformation during MHC-peptide binding. Currently, available algorithms are developed for protein sidechain prediction upon fixed backbone template. This study shows the preference of backbone atoms in MHC-peptide binding and hence emphasizes the need for accurate peptide backbone prediction in quantitative MHC-peptide binding calculations.

Binding Sites↗
PubMed1991

What indication is common to different genotoxicity data bases?

This paper studies the relationships among 4 in vitro assays: Salmonella mutation (STY), mouse lymphoma L5178Y cell mutation (MLY), chromosomal aberrations in CHO cells (CHA), and sister-chromatid exchanges in CHO cells (SCE), in 3 different data bases: U.S. National Toxicology Program (NTP), International Program for the Evaluation of Short-Term Tests for Carcinogens (IPESTTC), and International Program on Chemical Safety (IPCS). The analysis is performed by modeling each data base with factor analysis. With this tool, it has been possible to separate the different elements (or components) which play a role in each data base. It has also been possible to demonstrate that--together with some specificities of the data bases--there is a common effect which is independent of the data bases, and which typically represents the 'true' relationships among the assays. This element explains 69% of the information contained in NTP, 50% of that of IPESTTC, and 30% of that of IPCS. This common evidence indicates that the responses of STY and CHA to the 'universe' of chemicals are relatively similar, although STY is a bacterial mutation system and CHA is a mammalian cell test for chromosomal damage. The other similarity apparent from this analysis is the one between MLY (mutation in mouse cells) and SCE (cytogenetic evidence in hamster cells). The implication of this result is 2-fold. On the one hand, it is extremely reassuring that the 3 most important comparative studies agree and show common evidence, and this can be recognized rationally. On the other hand, this evidence implies that the scientists involved in mutagenicity research must face the task of exploring and explaining such relationships.

Animals↗
PubMed1997

Database and quick methods of assessing typical dietary fiber intakes using data for 228 commonly consumed foods.

To promote assessment of dietary fiber intakes in clinical settings, we established two objectives for this study: to provide a detailed database in grams per serving of fiber content and polymer composition for most fiber sources in the US diet, and to develop a quick method for estimating total fiber intakes. Data for 342 foods were condensed to 228 foods by combining similar foods. The comprehensive database developed includes pectin, hemicelluloses, and beta-glucan contents of the soluble and insoluble fractions of fiber and the cellulose and Klason lignin contents of the insoluble fiber. Three fourths of the 228 foods contained 2.0 g fiber per serving or less; only 10% contained more than 3.0 g per serving. The quick method consists of multiplying the number of servings in each food group by the mean total dietary fiber content of foods in that group: 1.5 g for fruits (n = 43), 1.5 g for vegetables (n = 68), 1.0 g for refined grains (n = 80), and 2.5 g for whole grains (n = 13). Actual fiber values from the database should be used in the quick method if foodstuffs concentrated from grains, legumes, and nuts and seeds are consumed. Sample menus demonstrate that quick assessment of total fiber intake yielded results similar to the sum of individual values from the database.

Databases, Factual↗
PubMed1999

Alternative medicine: what the data say about common herbal therapies.

An increasing number of Americans are turning to complementary and alternative medicine to help manage or prevent the onset of chronic disease, improve cognitive function, boost overall general well-being, and increase longevity. Some of the more widely-used herbal preparations designed to help accomplish these objectives include St. John's wort, ginkgo biloba, echinacea, garlic, and ginger. In general, the clinical trial data on these preparations is in the embryonic stages, whereas the popularity of these compounds is fueled in part by anecdotal evidence. Given the embrace by Americans--especially older persons--of these alternative remedies, knowledge of their uses and potential side effects can help the primary care physician better collaborate on a course of care that makes effective use of the best treatments, both traditional and alternative.

Aged↗
PubMed2003

A neural network-based similarity index for clustering DNA microarray data.

A common approach to the analysis of gene expression data is to define clusters of genes that have similar expression. A critical step in cluster analysis is the determination of similarity between the expression levels of two genes. We introduce a neural network-based similarity index as a non-linear similarity index and compare the results with other proximity measures for Saccharomyces cerevisiae gene expression data. We show that the clusters obtained using Euclidean distance, correlation coefficients, and mutual information were not significantly different. The clusters formed with the neural network-based index were more in agreement with those defined by functional categories and common regulatory motifs.

Algorithms↗
PubMed1997

GAW10: simulated family data for a common oligogenic disease with quantitative risk factors.

GAW10 Problem 2 involves a simulated common disease defined by imposing a threshold, T, on a quantitative trait, Q1. Every individual with a value of Q1 > or = T (where T = 40) is defined as affected. Also thought to be associated with the disease as intervening variables are four other quantitative traits (Q2, Q3, Q4, and Q5) and an environmental factor (EF). Each individual has genotypes for 367 highly polymorphic markers on 10 chromosomes. The tasks for GAW10 were to characterize the genetic and environmental contribution to Q1 (and the disease), Q2, Q3, Q4, and Q5, and to localize any single genes that have detectable effects. Multiple replicates provided an opportunity to address questions of power and false positive rates.

Chromosome Mapping↗
PubMed2003

Making the boundaries clearer: revisiting information systems with fading boundaries.

PURPOSE: To address issues of importance in 1994 and what has happened in those issues. METHODS: A number of questions and issues will be examined. Were we right in our focus at that time and what did we miss? What has happened that perhaps changed our perspectives and philosophies? Has the need changed? Is the model of fading boundaries a correct one, and how far have we gone in realizing a communication system in dealing with those boundaries? What progress have we made internationally on these issues? How are we working internationally to solve these problems? RESULTS: The fifth working conference relating to hospital information systems (HIS) was held in Durham, North Carolina in August 1994. The Institute of Medicine publication The Computer-based Patient Record: An Essential Technology for Health Care had been published in 1991 and had begun influencing thinking and direction for clinical information systems. The difference between and relationship of HIS and Computer-based Patients Records was the topic of much discussion and debate. The 1994 conference strongly recognized the need for standards specifically for data exchange, unique patient identifier, data definitions and common clinical data sets and for clinical terminology. Interconnectivity and interoperability were identified as separate but related problems to be solved. Technology was not considered to be a barrier, and projections for bandwidth to meet data dissemination requirements were favorable. In the 7 years after the Durham conference, many things have changed dramatically. Progress has been made in a number of areas, and some of the projections have been realized. However, it is surprising to note what areas still remain problems, particularly noting what problems have been worked on without success and what problems have not even been addressed. It is interesting to speculate that if the Durham conference was repeated today, would it be accepted as a current event?

Hospital Information Systems↗
PubMed2006

Cardiac rhythm management: the shape of things to come.

PURPOSE OF REVIEW: The aim of this article is to forecast a major imminent change in the clinical practice of cardiac rhythm management, which is argued to be remote patient monitoring, its potential benefits to clinical practitioners and its barriers to widespread diffusion. RECENT FINDINGS: All four major manufacturers of cardiac rhythm management devices have recently introduced varying types of systems that allow remote patient monitoring. These remote patient monitoring systems promise more efficient patient management in today's clinical setting of rapidly growing numbers of patients with increasingly heterogeneous etiology, varying indications and comorbidities. The major differences between current systems are related to the degree of patient involvement in remote patient monitoring and limits on patient mobility. Other important factors that influence the value of remote patient monitoring are the degree to which remote follow-up would completely fulfill the requirements of an in-office follow-up and the inclusion of sensors that enable the prediction of major clinical events such as heart failure decompensation with a high degree of accuracy. SUMMARY: Even if the different remote patient monitoring systems currently available offer several clinical benefits such as early detection of cardiac events and complications, reduced follow-up costs and increased safety, the full potential of such systems requires the possibility to easily transfer relevant patient data to common patient databases that are linked to hospital information systems or electronic patient records. Only then will it be possible to gain a complete picture of patient conditions. This will require the development of common protocols for data communication and may involve issues of patient data ownership and integrity.

Arrhythmias, Cardiac↗
PubMed1983

Influence of second-order data filtering on common forced expiration indices.

Forced expiratory manoeuvres are extensively recorded using flow meters coupled to pressure transducers, which usually behave like second-order filters. To assess what should be the dynamic characteristics of such equipment for accurate determination of common forced expiration indices, 125 curves were obtained from 25 healthy subjects in the best technical conditions. The flow-time curves were then submitted to various degrees of second-order filtering, and the indices derived from filtered and unfiltered curves were compared. Considering that experimental error is acceptable if it does not exceed 20% of the normal interindividual variability for 95% of the curves, the following conclusion was drawn; with an optimal damping ratio (r) of 0.7, forced expiratory volume in one second, maximum midexpiratory flow rate and maximal expiratory flow at 25% of the forced vital capacity (MEF25) are still correctly measured when the resonant frequency (fn) is as low as 3 Hz. The corresponding figures are 5 Hz for MEF50, 20 Hz for peak expiratory flow rate and above 20 Hz for MEF75. Higher values of fn are usually required when r is higher or lower than 0.7.

Adult↗