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Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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PubMed1990

Language learning efficiency, dreams and REM sleep.

As a follow-up from a previous study, four subjects taking a 6-week French language immersion program maintained a dream diary starting 2 weeks before until 2 weeks after the course. They also slept in the laboratory during four series of nights: one before the course, two during the course and one after the course. Confirming previous observations, it was observed that those subjects who made significant progress in French learning, experienced French incorporations into dreams earlier and had more verbal communication in their dreams during the language training than those who made little progress. Combining these results with those of the earlier study revealed significant positive correlations between language learning efficiency and both increases in REM sleep percentages, and verbal communication in dreams, as well as a negative correlation with latency to the first French incorporation in dreams. These results support the notion that REM sleep and dreaming are related to waking cognitive processes.

Adult↗

PubMed1994

A C++ framework for developing Medical Logic Modules and an Arden Syntax compiler.

When developing a clinical decision support system that uses knowledge expressed in Arden Syntax, the availability of a robust means of translating Arden Syntax into an executable module becomes critical. This paper describes an approach where Arden Syntax is translated into an intermediate pseudo-Arden language that is in turn compiled and linked to create the executable module. The pseudo-Arden language is defined in C++ using specialized class libraries and preprocessor macros. This approach provides an alternative means of developing the code generator for an Arden Syntax compiler.

Artificial Intelligence↗

PubMed2004

APE: Analyses of Phylogenetics and Evolution in R language.

UNLABELLED: Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. AVAILABILITY: The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.

Biological Evolution↗

PubMed2003

DICOM structured report document type definition.

The Digital Imaging and Communications in Medicine (DICOM) standard recently introduced rules for the encoding, transmission and storage of the structured diagnostic report. This medical document can be stored and communicated with the images. It has a structure and may contain text, with links to other data such as images, waveforms and spatial or temporal coordinates. The prompt availability of the radiology report is crucial for implementing a Patient Electronic Record. Using the extensible markup language (XML) to encode the radiology report broadens its accessibly. This paper presents a document type definition (DTD) that accurately models the DICOM structured report content, structure, and constraints.

Abstracting and Indexing↗

PubMed2000

Taxonomic markup language: applying XML to systematic data.

SUMMARY: An XML document type definition (DTD) is provided for the description of taxonomic relationships between organisms. Two XSL style-sheets for the graphical presentation of simple taxonomic trees are also provided. AVAILABILITY: The DTD and stylesheets along with sample files are available at http://www.albany.edu/gilmr/pubxml/.

Classification↗

PubMed2001

XML and the VITAL standard: the document-oriented approach for open telemedicine applications.

This paper describes an effort to create a common, document-oriented architecture for the interchange of medical data in healthcare telemedicine applications. Key components are: The VITAL standard specifying a common (medical device independent) representation of Vital Signs Information and the Extensible Markup Language (XML) specifying the document specifications form, an architecture that, in aggregate, define the semantics and structural constraints necessary for the exchange of vital signs and related medical data. The modelling and design technique for the described application has been the Unified Modelling Language (UML). The XMI (XML Metadata Interchange Format) of the Object Management Group (OMG) provided the meta-model for this application, for sharing objects using XML, via the transfer of the application's UML model to XML documents and DTDs.

Humans↗

PubMed2002

WITH: a system to write clinical trials using XML and RDBMS.

The paper illustrates the system WITH (Write on Internet clinical Trials in Haematology) which supports the writing of a clinical trial (CT) document. The requirements of this system have been defined analysing the writing process of a CT and then modelling the content of its sections together with their logical and temporal relationships. The system WITH allows: a) editing the document text; b) re-using the text; and c) facilitating the cooperation and the collaborative writing. It is based on XML mark-up language, and on a RDBMS. This choice guarantees: a) process standardisation; b) process management; c) efficient delivery of information-based tasks; and d) explicit focus on process design.

Clinical Trials as Topic↗

PubMed1989

Pattern conserving data structure and algorithms for computations on dendritic trees.

The linked list is offered as a pattern conserving data structure, useful for storing neuronal dendritic trees. A BASIC language algorithm is described. Modifications of this algorithm for building linked lists, graphing dendritic trees, and tarry ordering trees are presented. Brief mention is made of the last in first out stack as a alternative data structure for computations on dendritic trees.

Algorithms↗

PubMedDate not supplied

Design and implementation of a national clinical trials registry.

The authors have developed a Web-based system that provides summary information about clinical trials being conducted throughout the United States. The first version of the system, publicly available in February 2000, contains more than 4,000 records representing primarily trials sponsored by the National Institutes of Health. The impetus for this system has come from the Food and Drug Administration (FDA) Modernization Act of 1997, which mandated a registry of both federally and privately funded clinical trials "of experimental treatments for serious or life-threatening diseases or conditions." The system design and implementation have been guided by several principles. First, all stages of system development were guided by the needs of the primary intended audience, patients and other members of the public. Second, broad agreement on a common set of data elements was obtained. Third, the system was designed in a modular and extensible way, and search methods that take extensive advantage of the National Library of Medicine's Unified Medical Language System (UMLS) were developed. Finally, since this will be a long-term effort involving many individuals and organizations, the project is being implemented in several phases.

Clinical Trials as Topic↗

PubMed2006

Selecting biological data sources and tools with XPR, a path language for RDF.

As the number, richness and diversity of biological sources grow, scientists are increasingly confronted with the problem of selecting appropriate sources and tools. To address this problem, we have designed BioGuidel, a user-centric framework that helps scientists choose sources and tools according to their preferences and strategy, by specifying queries through a user-friendly visual interface. In this paper, we provide a complete RDF representation of BioGuide and introduce XPR (eXtensible Path language for RDF), an extension of FSL2 that is expressive enough to model all BioGuide queries. BioGuide queries modeled as XPR expressions can then be saved, compared, evaluated and exchanged through the Web between users and applications.

Computational Biology↗

PubMed1998

An XML portable chart format.

The clinical chart remains the fundamental record of outpatient clinical care. As this information migrates to electronic form, there is an opportunity to create standard formats for transmitting these charts. This paper describes work toward a Portable Chart Format (PCF) that can represent the relevant aspects of an outpatient chart. The main goal of the format is to provide a packaging medium for outpatient clinical charts in a transfer of care scenario. A secondary goal is to support the aggregation of comparable clinical data for outcomes analysis. The syntax used for PCF is Extended Markup Language (XML), a W3C standard. The structure of the PCF is based on a clinically relevant view of the data. The data definitions and nomenclature used are based primarily on existing clinical standards.

Humans↗

PubMed1974

Using preschool materials to modify the language of disadvantaged children.

Although language remediation programs have generally been conducted with the use of special materials in structured group settings, traditional preschool practice emphasizes "incidental teaching" incorporated into children's free play. To determine if incidental teaching practices could be effective in improving children's speech, this study investigated the spontaneous speech of 12 disadvantaged children during free-play periods over eight months of a preschool program. Whenever the children selected a preschool play material, they were prompted and required to ask for it, first by name (noun), then by name plus a word that described the material (adjective-noun combination), then by use of a color adjuctive-noun combination, and finally by requesting the material and describing how they were going to use it (compound sentence). As each requirement was made, the children's general use of that aspect of language markedly increased, but little change was noted in the amount or nature of the children's interactions with teachers or their use of a set of materials to which they had free access. This study demonstrates that preschool free-play periods can be powerful "incidental teaching" periods by capitalizing on moments when children seek new play materials.

Child, Preschool↗

PubMed1990

Client-server MUMPS takes on the future.

The early stages of MUMPS demonstrated the language's reliability and functionality, yet it was limited to operating on standalone mainframe and minicomputer architectures. Slowly, as technology progressed and client-server networks became a reality, the speed and performance of MUMPS has brought new dimensions to healthcare.

Computer Systems↗

PubMed2002

A proposed referral centre based on HL7/XML.

With the growth of the Inteernet, hospitals have also applied HL7 (Health Level Seven) to exchange data between them. The referral system is identified as an appropriate application system. The effect of referral is to transfer the patient to a suitable hospital in a timely fashion, and to arrange appropriate treatment for the patient. Taking advantage of the Internet to exchange referral data can, not only accelerate the process of patient referral, but also avoid the unnecessary repeat examinations to decrease the waste of medical resources. This article builds up a referral-related message according to the HL7 standard, and develops a referral centre using the Internet environment, making use of XML (eXtensible Markup Language) standard to transform the referral-related data to XML format and exchange referral data between platforms. This electronic referral mechanism is expected to offer other hospitals experience of improved referral practice.

Access to Information↗

PubMed1995

Virtual reality modeling language in chemistry.

A new concept in the field of molecular modeling using the information transfer mechanism of the World Wide Web (WWW) is presented. The Virtual Reality Modeling Language (VRML) provides an object-oriented method for the description of molecular models. The structure and capabilities of this new language are introduced. It is shown that the transport of molecular models over the WWW using VRML is a very efficient and powerful method for the exchange of molecular information.

Computer Communication Networks↗

PubMed2001

Handling expressiveness and comprehensibility requirements in GLIF3.

Clinical guidelines are aimed at standardizing patient care and improving its quality and cost effectiveness. Guidelines represented in a computer-interpretable (CI) format can be used to provide automatic decision support applied to individual patients during the clinical encounter. The process of creating computer-interpretable guidelines (CIG) re-moves ambiguities contained in paper-based guidelines, thus making the guideline more comprehensible. For these reasons, CIGs may have a larger impact on clinician behavior than paper-based guidelines. Since much effort goes into creating guidelines in a CI format, it is desirable that different institutions and software systems share them. In a guideline representation workshop hosted by the InterMed Collaboratory in March 2000, the need for a standard representation format for sharable CIGs was recognized. As a first step towards achieving this goal, we proposed a set of functional requirements for sharable CIGs. The requirements encompass the entire life cycle of a CIG: development, implementation, use and maintenance. In this paper we discuss requirements that are important during the development stage of a CIG. We have abstracted the requirements into two groups: expressiveness--the ability to ex-press the knowledge content of different types of guidelines--and comprehensibility--the ability to manage complexity, facilitate coherence, and visualize a guideline model to aid in human comprehension. The Guideline Interchange For-mat version 3 (GLIF3) is a language for structured representation of CIGs. It is under development to facilitate sharing CIGs among different institutions and systems. We illustrate how GLIF3 meets the specified development requirements.

Decision Making, Computer-Assisted↗

PubMedDate not supplied

Representing medical knowledge: reconciling the present or creating the future?

Modern technology has sparked the creation of computing systems that perform many medically related tasks, but communication between these systems is limited, in part by differences in the terminology used for various purposes and in part by the changing nature of medical concepts. The Unified Medical Language System represents an attempt to find a means of translation between diverse knowledge systems. An alternative, which we propose, is to agree on a knowledge base for the future and make use of present accomplishments in moving toward that goal.

Abstracting and Indexing↗

PubMed1993

Representation for discovery of protein motifs.

There are several dimensions and levels of complexity in which information on protein motifs may be available. For example, one-dimensional sequence motifs may be associated with secondary structure identifiers. Alternatively, three-dimensional information on polypeptide segments may be used to induce prototypical three-dimensional structure templates. This paper surveys various representations encountered in the protein motif discovery literature. Many of the representations are based on incompatible semantics, making difficult the comparison and combination of previous results. To make better use of machine learning techniques and to provide for an integrated knowledge representation framework, a general representation language--in which all types of motifs can be encoded and given a uniform semantics--is required. In this paper we propose such a model, called a spatial description logic, and present a machine learning approach based on the model.

Amino Acids↗