PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Programming Languages”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,711 records · Page 95Linked to original sources
PubMed1989

Incidence density matching with a simple SAS computer program.

Incidence density matching is the method of choice for selecting controls in nested case-control studies, but its use has been limited by its computational complexity. We describe incidence density matching in nested case-control studies with a simple and flexible SAS computer program. The program contains no restrictions on the number of matching factors, although it is usually only necessary to match on age (in incidence density fashion) and on gender. The program is illustrated with data from an historical cohort study of the mortality experience of workers at an asbestos textile manufacturing plant.

Case-Control Studies↗
PubMed1997

A simple program to create exact person-time data in cohort analyses.

BACKGROUND: Before disease rates can be calculated a tabulation of the length of follow-up for each person in the cohort has to be made. In complicated analyses such tabulations are often stratified by many characteristics, some which show no change with time, such as gender or year of birth, and some which do change with time, such as age or cumulative exposure. Available computer programs often restrict the way these tables can be made, particularly when handling time-dependent variables. METHODS: This paper presents a simple computer program which calculates the length of follow-up for each person in a study. RESULTS: Person-time data can be tabulated by a large number of variables using this method. This program is extremely flexible in the way that time-dependent variables can be created, can categorize observations by any unit of person-time, and will run on a range of platforms including a personal computer. CONCLUSIONS: This method should simplify the task of creating person-time data for analyses of disease rates in epidemiological studies.

Cohort Studies↗
PubMed1988

An RNA secondary structure workbench.

A multiple approach to the study of RNA secondary structure is described which provides for the independent drawing of structures using base-pairing lists, for the generation of local structures in the form of hairpins, and for the generation of global structures by both Monte Carlo and dynamic programming methodologies. User-adjustable parameters provide for limiting the size of hairpin loops, bulges and inner loops, and constraints can be imposed relative to position-dependent base pairing.

Algorithms↗
PubMed2001

Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs.

The HIV Reverse Transcriptase and Protease Sequence Database is an on-line relational database that catalogs evolutionary and drug-related sequence variation in the human immunodeficiency virus (HIV) reverse transcriptase (RT) and protease enzymes, the molecular targets of anti-HIV therapy (http://hivdb.stanford.edu). The database contains a compilation of nearly all published HIV RT and protease sequences, including submissions from International Collaboration databases and sequences published in journal articles. Sequences are linked to data about the source of the sequence sample and the antiretroviral drug treatment history of the individual from whom the isolate was obtained. During the past year 3500 sequences have been added and the data model has been expanded to include drug susceptibility data on sequenced isolates. Database content has also been integrated with didactic text and the output of two sequence analysis programs.

Amino Acid Sequence↗
PubMed2001

The life sciences Global Image Database (GID).

Although a vast amount of life sciences data is generated in the form of images, most scientists still store images on extremely diverse and often incompatible storage media, without any type of metadata structure, and thus with no standard facility with which to conduct searches or analyses. Here we present a solution to unlock the value of scientific images. The Global Image Database (GID) is a web-based (http://www.gwer.ch/qv/gid/gid.ht m ) structured central repository for scientific annotated images. The GID was designed to manage images from a wide spectrum of imaging domains ranging from microscopy to automated screening. The annotations in the GID define the source experiment of the images by describing who the authors of the experiment are, when the images were created, the biological origin of the experimental sample and how the sample was processed for visualization. A collection of experimental imaging protocols provides details of the sample preparation, and labeling, or visualization procedures. In addition, the entries in the GID reference these imaging protocols with the probe sequences or antibody names used in labeling experiments. The GID annotations are searchable by field or globally. The query results are first shown as image thumbnail previews, enabling quick browsing prior to original-sized annotated image retrieval. The development of the GID continues, aiming at facilitating the management and exchange of image data in the scientific community, and at creating new query tools for mining image data.

Biological Science Disciplines↗
PubMed1997

Power and sample size calculations for case-control studies of gene-environment interactions with a polytomous exposure variable.

Genetic polymorphisms may appear to the epidemiologist most commonly as different levels of susceptibility to exposure. Epidemiologic studies of heterogeneity in exposure susceptibility aim at estimating the parameter quantifying the gene-environment interaction. In this paper, the authors use a general approach to power and sample size calculations for case-control studies, which is applicable to settings where the exposure variable is polytomous and where the assumption of independence between the distribution of the genotype and the environmental factor may not be met. It was found through exploration of different scenarios that in the cases explored, power calculations were relatively insensitive to assumptions about the odds ratio for the exposure in the referent genotype category and to assumptions about the odds ratio for the genetic factor in the lowest exposure category, yet they were relatively sensitive to assumptions about gene frequency, particularly when gene frequency was low. In general, to detect a small to moderate gene-environment interaction effect, large sample sizes are needed. Because the examples studied represent only a small subset of possible scenarios that could occur in practice, the authors encourage the use of their user-friendly Fortran program for calculating power and sample size for gene-environment interactions with exposures grouped by quantiles that are explicitly tailored to the study at hand.

Case-Control Studies↗
PubMed1998

A visual environment for the manipulation and integration of JAVA beans.

MOTIVATION: Visual programming has the potential to allow non-programmers to redesign and rebuild applications to suit their individual needs. We have built such a visual programming environment, which allows non-programmers to interrogate and combine software components graphically to form new applications. As the needs of the biological community grow, so too will the need for more powerful and easy to use software tools. Intelligent visual programming environments will allow users to design and develop applications easily, so that they can concentrate on the application they wish to build rather than how it is to be done. RESULTS: The environment can read in JAVA Beans, and present relevant information about the beans to the user. The user can then graphically specify how they would like information to flow between the beans by performing simple docking operations. Unnecessary complexities associated with such visual design have been removed by providing intelligent docking of components and visual feedback. With such mechanisms, the complexities of building new applications are reduced. When the biologist has finished the visual construction, the design system is able to generate the new application automatically. The system has been designed specifically to meet the needs of the biological community, and a range of 'BioBeans' are being developed. These include beans for visualization (sequence displays and data visualizers), analysis (feature recognition, error detection) and communication (database access, URL retrieval, DDE communication). AVAILABILITY: Freely available. CONTACT: boyle@synomics.com

Computational Biology↗
PubMed1996

Motivational factors in learning American sign lanquage.

This study focuses on factors that motivate and demotivate professionals to learn American Sign Language (ASL). Using a qualitative approach known as the Critical Incident Technique (CIT), faculty and staff were asked to reflect on their sign language learning expericences, and their responses were examined for motivational patterns. Principal motivating factors were intrinsic in nature, including a desire to perform well in one's position, personal goals, and an interest in sign language per se. Integrative factors were also important, especially an interest in social interactions with deaf people. Principal factors that demotivated the respondents were more extrinsic in nature, dealing with workload, scheduling issues associated with the sign language curriculum, instruction, and the attitudes of self and others. We draw implications from the findings for the enhancement of sign language instruction programs.

Journal Article↗
PubMed2006

Treating voxel geometries in radiation protection dosimetry with a patched version of the Monte Carlo codes MCNP and MCNPX.

The question of Monte Carlo simulation of radiation transport in voxel geometries is addressed. Patched versions of the MCNP and MCNPX codes are developed aimed at transporting radiation both in the standard geometry mode and in the voxel geometry treatment. The patched code reads an unformatted FORTRAN file derived from DICOM format data and uses special subroutines to handle voxel-to-voxel radiation transport. The various phases of the development of the methodology are discussed together with the new input options. Examples are given of employment of the code in internal and external dosimetry and comparisons with results from other groups are reported.

Body Burden↗
PubMedDate not supplied

Medical computing over the World Wide Web: use of forms and CGI scripts for constructing medical algorithm Web pages.

The development of the World Wide Web has led to an explosion of educational and clinical resources available via the Internet with minimal effort or special training. However, most of these Web pages contain only static information; few offer dynamic information shaped around clinical or laboratory test findings. In this report we show how this goal can be achieved with the design and construction of Medical Algorithm Web Pages (MAWP). Specifically, using Internet technologies known as forms and CGI scripts we demonstrate how one can implement medical algorithms remotely over the Internet's World Wide Web. To use a MAWP, one enters the URL for the site and then enters information according to the instructions presented there, usually by entering numbers and other information into fields displayed on screen. When all the data is entered, the user clicks on the SUBMIT icon, resulting in a new Web page being constructed "on-the-fly" containing diagnostic calculations and other information pertinent to the patient's clinical management. Four sample applications are presented in detail to illustrate the concept of a Medical Algorithm Web page: Computation of the alveolar-arterial oxygen tension difference using the alveolar gas equation; Computation of renal creatinine clearance; drug infusion calculation (micrograms/kilogram/minute); Computation of the renal failure index.

Algorithms↗
PubMedDate not supplied

Automated image registration: I. General methods and intrasubject, intramodality validation.

PURPOSE: We sought to describe and validate an automated image registration method (AIR 3.0) based on matching of voxel intensities. METHOD: Different cost functions, different minimization methods, and various sampling, smoothing, and editing strategies were compared. Internal consistency measures were used to place limits on registration accuracy for MRI data, and absolute accuracy was measured using a brain phantom for PET data. RESULTS: All strategies were consistent with subvoxel accuracy for intrasubject, intramodality registration. Estimated accuracy of registration of structural MRI images was in the 75 to 150 microns range. Sparse data sampling strategies reduced registration times to minutes with only modest loss of accuracy. CONCLUSION: The registration algorithm described is a robust and flexible tool that can be used to address a variety of image registration problems. Registration strategies can be tailored to meet different needs by optimizing tradeoffs between speed and accuracy.

Algorithms↗