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Quality and accountability in the ESRD program.

The quality of care received by patients with end-stage renal disease (ESRD) in the United States has received considerable public attention during the past several years because of a number of social, economic, and political factors. There has been a lingering impression that the poorer survival of dialysis patients in the United States, compared with their counterparts in other industrialized countries, is because of process factors for which there are opportunities for improvement, rather than just an adverse case mix. Recent reports by the Office of the Inspector General and the General Accounting Office have recommended that the Health Care Financing Administration (HCFA) improve its oversight of dialysis providers and hold the providers more accountable for their patient care outcomes. This requires the development of validated clinical performance measures that, in turn, should be derived from evidence-based clinical practice guidelines. The dual oversight model, with the state survey agencies agencies performing a quality assurance function to require facilities to meet minimal standards of operation (Medicare's conditions of participation) to prevent patient harm, and with the ESRD Networks performing a quality improvement function to bring processes and outcomes for all patients to a higher level, appears to be sound. HCFA's move toward increased provider accountability has included the development of facility-specific profiles for processes of care (dialysis adequacy) and outcomes (hemoglobin level and standardized mortality ratio), which may trigger state surveyor activities and that will be available for public scrutiny on a HCFA-sponsored web site. The adoption and application of continuous quality improvement methodologies at the dialysis provider level will be an important strategy for favorably positioning the facility in a competitive and demanding health care marketplace.

Humans↗

Taking the guesswork out of mandibular symphyseal distraction osteogenesis.

Mandibular symphyseal distraction osteogenesis has recently been introduced as a means of resolving arch length deficiencies in the anterior segment and as a method of reducing large vestibular spaces related to a narrow mandible. Accurately relating the required distraction for a given anterior tooth mass and desired future anteroposterior location of the central incisors has not been possible until recently. The relationship between these 3 controlling factors has been mathematically described by the hyperbolic cosine function and a computer program designed for easy use by the clinician. Two clinical cases illustrate the application of the program. A Web site where the program can be downloaded at no cost is mentioned.

Algorithms↗

A novel method for GPCR recognition and family classification from sequence alone using signatures derived from profile hidden Markov models.

G-protein coupled receptors (GPCRs) constitute a broad class of cell-surface receptors, including several functionally distinct families, that play a key role in cellular signalling and regulation of basic physiological processes. GPCRs are the focus of a significant amount of current pharmaceutical research since they interact with more than 50% of prescription drugs, whereas they still comprise the best potential targets for drug design. Taking into account the excess of data derived by genome sequencing projects, the use of computational tools for automated characterization of novel GPCRs is imperative. Typical computational strategies for identifying and classifying GPCRs involve sequence similarity searches (e.g. BLAST) coupled with pattern database analysis (e.g. PROSITE, BLOCKS). The diagnostic method presented here is based on a probabilistic approach that exploits highly discriminative profile Hidden Markov Models, excised from low entropy regions of multiple sequence alignments, to derive potent family signatures. For a given query, a P-value is obtained, combining individual hits derived from the same family. Hence a best-guess family membership is depicted, allowing GPCRs' classification at a family level, solely using primary structure information. A web-based version of the application is freely available at URL: http:/bioinformatics.biol.uoa.gr/PRED-GPCR.

Databases, Factual↗

Talisman--rapid application development for the grid.

In order to make use of the emerging grid and network services offered by various institutes and mandated by many current research projects, some kind of user accessible client is required. In contrast with attempts to build generic workbenches, Talisman is designed to allow a bioinformatics expert to rapidly build custom applications, immediately visible using standard web technology, for users who wish to concentrate on the biology of their problem rather than the informatics aspects. As a component of the MyGrid project, it is intended to allow access to arbitrary resources, including but not limited to relational, object and flat file data sources, analysis programs and grid based storage, tracking and distributed annotation systems.

Computational Biology↗

A computational pipeline for protein structure prediction and analysis at genome scale.

MOTIVATION: Experimental techniques alone cannot keep up with the production rate of protein sequences, while computational techniques for protein structure predictions have matured to such a level to provide reliable structural characterization of proteins at large scale. Integration of multiple computational tools for protein structure prediction can complement experimental techniques. RESULTS: We present an automated pipeline for protein structure prediction. The centerpiece of the pipeline is our threading-based protein structure prediction system PROSPECT. The pipeline consists of a dozen tools for identification of protein domains and signal peptide, protein triage to determine the protein type (membrane or globular), protein fold recognition, generation of atomic structural models, prediction result validation, etc. Different processing and prediction branches are determined automatically by a prediction pipeline manager based on identified characteristics of the protein. The pipeline has been implemented to run in a heterogeneous computational environment as a client/server system with a web interface. Genome-scale applications on Caenorhabditis elegans, Pyrococcus furiosus and three cyanobacterial genomes are presented. AVAILABILITY: The pipeline is available at http://compbio.ornl.gov/proteinpipeline/

Algorithms↗

Web-based networking in CNS education.

PURPOSE: An important component of the clinical nurse specialist (CNS) educational program involves anticipatory guidance for students assimilating the CNS role. This article describes a strategy for facilitating this transition through online discussion about CNS practice among students and experienced CNSs. DESCRIPTION OF THE PROCESS: Six students in the final semester of their CNS program and 5 CNSs from across the country used the WebCT platform to participate in an online learning experience. This article outlines the process of structuring an online discussion, soliciting an expert panel, and preparing the participants. Students' concerns and panelists' responses are presented. CONCLUSIONS: Themes that emerged from students' questions to the panelists were certification and title protection; developing a career trajectory, including tips for interviewing and negotiation; and current and future trends in CNS practice. Benefits to participants are described, as well as suggestions for using Web-based discussion in other applications.

Attitude of Health Personnel↗

Computer-based ambulatory information systems: recent developments.

This article updates the author's earlier review of some of the major computer-based ambulatory information systems and the literature evaluating their costs, benefits, effect on quality of care, and physician acceptance. The evidence suggests that computer-based information systems can increase access to clinical information, improve physician performance, enhance quality of care, and facilitate outcomes research review. In addition to presenting health information networks and clinical decision support systems such as reminder systems, drug ordering systems, and medical care management systems, the article describes applications of telemedicine and Web-based systems. It also discusses barriers to the widespread use of computer-based ambulatory information systems.

Ambulatory Care Information Systems↗

BLAT--the BLAST-like alignment tool.

Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. A new tool, BLAT, is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. BLAT's speed stems from an index of all nonoverlapping K-mers in the genome. This index fits inside the RAM of inexpensive computers, and need only be computed once for each genome assembly. BLAT has several major stages. It uses the index to find regions in the genome likely to be homologous to the query sequence. It performs an alignment between homologous regions. It stitches together these aligned regions (often exons) into larger alignments (typically genes). Finally, BLAT revisits small internal exons possibly missed at the first stage and adjusts large gap boundaries that have canonical splice sites where feasible. This paper describes how BLAT was optimized. Effects on speed and sensitivity are explored for various K-mer sizes, mismatch schemes, and number of required index matches. BLAT is compared with other alignment programs on various test sets and then used in several genome-wide applications. http://genome.ucsc.edu hosts a web-based BLAT server for the human genome.

Animals↗

The International Rice Information System. A platform for meta-analysis of rice crop data.

Ambiguous germplasm identification; difficulty in tracing pedigree information; and lack of integration between genetic resources, characterization, breeding, evaluation, and utilization data are constraints in developing knowledge-intensive crop improvement programs. To address these constraints, the International Crop Information System (www.icis.cgiar.org), a database system for the management and integration of global information on genetic resources and crop improvement for any crop, was developed by genetic resource specialists, crop scientists, and information technicians associated with the Consultative Group for International Agricultural Research and collaborative partners. The International Rice Information System (www.iris.irri.org) is the rice (Oryza species) implementation of the International Crop Information System. New components are now being added to the International Rice Information System to handle the diversity of rice functional genomics data including genomic sequence data, molecular genetic data, expression data, and proteomic information. Users access information in the database through stand-alone programs and Web interfaces, which offer specialized applications and customized views to researchers with different interests.

Breeding↗

Visual analysis of large heterogeneous social networks by semantic and structural abstraction.

Social network analysis is an active area of study beyond sociology. It uncovers the invisible relationships between actors in a network and provides understanding of social processes and behaviors. It has become an important technique in a variety of application areas such as the Web, organizational studies, and homeland security. This paper presents a visual analytics tool, OntoVis, for understanding large, heterogeneous social networks, in which nodes and links could represent different concepts and relations, respectively. These concepts and relations are related through an ontology (also known as a schema). OntoVis is named such because it uses information in the ontology associated with a social network to semantically prune a large, heterogeneous network. In addition to semantic abstraction, OntoVis also allows users to do structural abstraction and importance filtering to make large networks manageable and to facilitate analytic reasoning. All these unique capabilities of OntoVis are illustrated with several case studies.

Algorithms↗

Multiple sclerosis medical image analysis and information management.

Magnetic resonance imaging (MRI) has become a central tool for patient management, as well as research, in multiple sclerosis (MS). Measurements of disease burden and activity derived from MRI through quantitative image analysis techniques are increasingly being used. There are many complexities and challenges in building computerized processing pipelines to ensure efficiency, reproducibility, and quality control for MRI scans from MS patients. Such paradigms require advanced image processing and analysis technologies, as well as integrated database management systems to ensure the most utility for clinical and research purposes. This article reviews pipelines available for quantitative clinical MRI research in MS, including image segmentation, registration, time-series analysis, performance validation, visualization techniques, and advanced medical imaging software packages. To address the complex demands of the sequential processes, the authors developed a workflow management system that uses a centralized database and distributed computing system for image processing and analysis. The implementation of their system includes a web-form-based Oracle database application for information management and event dispatching, and multiple modules for image processing and analysis. The seamless integration of processing pipelines with the database makes it more efficient for users to navigate complex, multistep analysis protocols, reduces the user's learning curve, reduces the time needed for combining and activating different computing modules, and allows for close monitoring for quality-control purposes. The authors' system can be extended to general applications in clinical trials and to routine processing for image-based clinical research.

Humans↗

The GATO gene annotation tool for research laboratories.

Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO) is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB.

Biomedical Research↗

An information-driven approach to pharmacogenomics.

Effective information management of the pharmacogenomics discipline presents many unique challenges. Genetic and genomic data generated via high-throughput methods need to be integrated with phenotypic data which are defined at multiscale levels, ranging from the molecular to the clinical level. Repositories storing these data are distributed and vary in terms of syntax and semantics which result in issues concerning data exchange and integration. The application of the emerging semantic web offers a promising solution to these interoperability issues.

Animals↗

A component-based, distributed object services architecture for a clinical workstation.

Attention to an architectural framework in the development of clinical applications can promote reusability of both legacy systems as well as newly designed software. We describe one approach to an architecture for a clinical workstation application which is based on a critical middle tier of distributed object-oriented services. This tier of network-based services provides flexibility in the creation of both the user interface and the database tiers. We developed a clinical workstation for ambulatory care using this architecture, defining a number of core services including those for vocabulary, patient index, documents, charting, security, and encounter management. These services can be implemented through proprietary or more standard distributed object interfaces such as CORBA and OLE. Services are accessed over the network by a collection of user interface components which can be mixed and matched to form a variety of interface styles. These services have also been reused with several applications based on World Wide Web browser interfaces.

Computer Communication Networks↗

School nurse web authoring.

Many school nurses are now surfing the World Wide Web for clinical and professional information. The Web is also a tool for providing professional services and delivering nursing care. Three applications for school nursing are featured: using the Web for professional publishing, a state association web page, and a school nurse office website.

Authorship↗

Multimedia technologies in education.

In general multimedia is the combination of visual and audio representations. These representations could include elements of texts, graphic arts, sound, animation, and video. However, multimedia is restricted in such systems where information is digitalized and is processed by a computer. Interactive multimedia and hypermedia consist of multimedia applications that the user has more active role. Education is perhaps the most useful destination for multimedia and the place where multimedia has the most effective applications, as it enriches the learning process. Multimedia both in nursing education and in medical informatics education has several applications as well. A multimedia project can be developed even as a "stand alone" application (on CD-ROM), or on World Wide Web pages on Internet. However several technical constraints exist for developing multimedia applications on Internet. For developing multimedia projects we need hardware and software, talent and skill. The software requirements for multimedia development consist of one or more authoring systems and various editing applications for text, images, sounds and video. In this chapter different software tools for creating multimedia applications are presented. In the last part of this chapter, two examples of multimedia educational training programs are discussed. Both are "stand alone" applications (CD-ROMs). The first, examines several aspects of the electronic patient record by using videos, audio descriptions, lectures and glossary, while the second one presents several topics regarding epidemiology and epidemiological research by using graphics, sound and animation.

CD-ROM↗

A problem-based learning trial on the Internet involving undergraduate nursing students.

This article describes the application of a nursing educational program developed on the basis of problem-based learning (PBL) and Internet technology, and reports student satisfaction and perceived learning effectiveness. This study was conducted in two phases-the development of a Web-based educational program and the application of this program using PBL strategies to teach undergraduate nursing students. The results showed this program was an effective method of delivering PBL to nursing students and the interaction between tutors and students influenced student satisfaction and learning effectiveness.

Adult↗

The diagnosis related groups enhanced electronic medical record.

PROBLEM: The introduction of Diagnosis Related Groups as a basis for hospital payment in Germany announced essential changes in the hospital reimbursement practice. A hospital's economical survival will depend vitally on the accuracy and completeness of the documentation of DRG relevant data like diagnosis and procedure codes. In order to enhance physicians' coding compliance, an easy-to-use interface integrating coding tasks seamlessly into clinical routine had to be developed. A generic approach should access coding and clinical guidelines from different information sources. METHODS: Within the Electronic Medical Record (EMR) a user interface ('DRG Control Center') for all DRG relevant clinical and administrative data has been built. A comprehensive DRG-related web site gives online access to DRG grouping software and an electronic coding expert. Both components are linked together using an application supporting bi-directional communication. Other web based services like a guideline search engine can be integrated as well. RESULTS: With the proposed method, the clinician gains quick access to context sensitive clinical guidelines for appropriate treatment of his/her patient and administrative guidelines for the adequate coding of the diagnoses and procedures. This paper describes the design and current implementation and discusses our experiences.

Diagnosis-Related Groups↗