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PubMed1998

Designing HeartCare: custom computerized home care for patients recovering from CABG surgery.

With the current trend toward discharge of cardiac artery bypass graft (CABG) patients from the hospital after 5 days, clinicians must make effective use of existing computer technology to provide more efficiently the services once available during the patient's lengthier hospital stay. This paper describes the design of the HeartCare initiative, a computerized cardiac recovery service designed to provide home-care support for patients in the first three months following CABG surgery. Capitalizing on the expansion in health resources on the Internet, and building on the lessons from the ComputerLink projects, HeartCare will employ the World Wide Web platform in the generation of personalized in-home computerized access to recovery resources. Key implementation decisions include selection of WebTV/ as the home-based device, and application of Metadata to organizing health-related knowledge resources on the WWW.

Computers↗

PubMed2006

Arachnid toxinology in Australia: from clinical toxicology to potential applications.

The unique geographic isolation of Australia has resulted in the evolution of a distinctive range of Australian arachnid fauna. Through the pioneering work of a number of Australian arachnologists, toxinologists, and clinicians, the taxonomy and distribution of new species, the effective clinical treatment of envenomation, and the isolation and characterisation of the many distinctive neurotoxins, has been achieved. In particular, work has focussed on several Australian arachnids, including red-back and funnel-web spiders, paralysis ticks, and buthid scorpions that contain neurotoxins capable of causing death or serious systemic envenomation. In the case of spiders, species-specific antivenoms have been developed to treat envenomed patients that show considerable cross-reactivity. Both in vitro and clinical case studies have shown they are particularly efficacious in the treatment of envenomation by spiders even from unrelated families. Despite their notorious reputation, the high selectivity and potency of a unique range of toxins from the venom of Australian arachnids will make them invaluable molecular tools for studies of neurotransmitter release and vesicle exocytosis as well as ion channel structure and function. The venoms of funnel-web spiders, and more recently Australian scorpions, have also provided a previously untapped rich source of insect-selective neurotoxins for the future development of biopesticides and the characterisation of previously unvalidated insecticide targets. This review provides a historical viewpoint of the work of many toxinologists to isolate and characterise just some of the toxins produced by such a unique group of arachnids and examines the potential applications of these novel peptides.

Animals↗

PubMed2005

CiteSpace II: visualization and knowledge discovery in bibliographic databases.

This article presents a description and case study of CiteSpace II, a Java application which supports visual exploration with knowledge discovery in bibliographic databases. Highly cited and pivotal documents, areas of specialization within a knowledge domain, and emergence of research topics are visually mapped through a progressive knowledge domain visualization approach to detecting and visualizing trends and patterns in scientific literature. The test case in this study is progressive knowledge domain visualization of the field of medical informatics. Datasets based on publications from twelve journals in the medical informatics field covering the time period from 1964-2004 were extracted from PubMed and Web of Science (WOS) and developed as testbeds for evaluation of the CiteSpace system. Two resulting document-term co-citation and MeSH term co-occurrence visualizations are qualitatively evaluated for identification of pivotal documents, areas of specialization, and research trends. Practical applications in bio-medical research settings are discussed.

Algorithms↗

PubMedDate not supplied

Conservation and management applications of the REEF volunteer fish monitoring program.

The REEF Fish Survey Project is a volunteer fish monitoring program developed by the Reef Environmental Education Foundation (REEF). REEF volunteers collect fish distribution and abundance data using a standardized visual method during regular diving and snorkeling activities. Survey data are recorded on preprinted data sheets that are returned to REEF and optically digitized. Data are housed in a publicly accessible database on REEF's Web site (http://www.reef.org). Since the project's inception in 1993, over 40,000 surveys have been conducted in the coastal waters of North America, tropical western Atlantic, Gulf of California and Hawaii. The Fish Survey Project has been incorporated into existing monitoring programs through partnerships with government agencies, scientists, conservation organizations, and private institutions. REEF's partners benefit from the educational value and increased stewardship resulting from volunteer data collection. Applications of the data include an evaluation of fish/habitat interactions in the Florida Keys National Marine Sanctuary, the development of a multi-species trend analysis method to identify sites of management concern, assessment of the current distribution of species, status reports on fish assemblages of marine parks, and the evaluation of no-take zones in the Florida Keys. REEF's collaboration with a variety of partners, combined with the Fish Survey Project's standardized census method and database management system, has resulted in a successful citizen science monitoring program.

Animals↗

PubMed1993

Inhibition of endogenous glutamate release from hippocampal tissue by Ca2+ channel toxins.

The pharmacology of voltage-dependent Ca2+ channels involved in the release of endogenous neurotransmitter amino acids was measured from small tissue slices of rat hippocampal CA1 region. Application of 50 mM KCl induced large increases in Ca(2+)-dependent overflow of endogenous glutamate, aspartate and gamma-aminobutyric acid (GABA). Pretreatment of tissues with the funnel-web spider toxin omega-Aga-IVA (200 nM) reduced KCl-induced overflow of all three amino acids. Pretreatment with the cone snail toxin omega-CgTx-GVIA (2 microM) caused similar but smaller reductions in amino acid overflow (aspartate overflow was not reduced significantly). These results indicate that P-type Ca2+ channels, and to a lesser extent, N-type Ca2+ channels, are involved in the release of transmitter amino acids under these conditions.

Animals↗

PubMed2003

Fluorescence: basic concepts, practical aspects, and some anecdotes.

We hope that we have conveyed information of interest and value to present and future fluorescence practitioners. Those readers with a sustaining interest in this topic may wish to consult more comprehensive sources such as Molecular Fluorescence: Principles and Applications, an excellent text by Valeur, or Principles of Fluorescence Spectroscopy by Lakowicz. Many specialized fluorescence topics are covered in the series Topics in Fluorescence Spectroscopy (Volumes 1-6), and several volumes of Methods in Enzymology (e.g., Volumes 246 and 278) have dealt with issues in fluorescence spectroscopy. Proceedings from the International Conference on Methods and Applications of Fluorescence Spectroscopy, 1997 (MAFS 97) and MAFS 98 (in press) also present fluorescence work on many different topics in biological and chemical fields. The Molecular Probes Handbook and web site (www.probes.com) are also rich sources of useful information. Finally, any reader with a question or seeking advice on some topic related to fluorescence is welcome to e-mail D.M.J. at djameson@hawaii.edu.

Energy Transfer↗

PubMed2000

Applying for grant funds: there's help around the corner.

Scientists should know where to get help when they write grant proposals. Books, videos, consultants and colleagues can all be useful. The World Wide Web is an excellent resource for finding competitors, collaborators and a wealth of other useful information such as funding agencies, available grant money, pertinent articles and form pages for grant applications. Software is available to help you make an outline of your proposal, prepare the required figures and tables and build a database of references from which to create a bibliography. This article will point you in the right direction for a plethora of information and resources.

Information Services↗

PubMed2006

Protein structure evaluation using an all-atom energy based empirical scoring function.

Arriving at the native conformation of a polypeptide chain characterized by minimum most free energy is a problem of long standing interest in protein structure prediction endeavors. Owing to the computational requirements in developing free energy estimates, scoring functions--energy based or statistical--have received considerable renewed attention in recent years for distinguishing native structures of proteins from non-native like structures. Several cleverly designed decoy sets, CASP (Critical Assessment of Techniques for Protein Structure Prediction) structures and homology based internet accessible three dimensional model builders are now available for validating the scoring functions. We describe here an all-atom energy based empirical scoring function and examine its performance on a wide series of publicly available decoys. Barring two protein sequences where native structure is ranked second and seventh, native is identified as the lowest energy structure in 67 protein sequences from among 61,659 decoys belonging to 12 different decoy sets. We further illustrate a potential application of the scoring function in bracketing native-like structures of two small mixed alpha/beta globular proteins starting from sequence and secondary structural information. The scoring function has been web enabled at www.scfbio-iitd.res.in/utility/proteomics/energy.jsp.

Computer Simulation↗

PubMed2002

Rat Genome Database (RGD): mapping disease onto the genome.

The Rat Genome Database (RGD, http://rgd.mcw.edu) is an NIH-funded project whose stated mission is 'to collect, consolidate and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community'. In a collaboration between the Bioinformatics Research Center at the Medical College of Wisconsin, the Jackson Laboratory and the National Center for Biotechnology Information, RGD has been created to meet these stated aims. The rat is uniquely suited to its role as a model of human disease and the primary focus of RGD is to aid researchers in their study of the rat and in applying their results to studies in a wider context. In support of this we have integrated a large amount of rat genetic and genomic resources in RGD and these are constantly being expanded through ongoing literature and bulk dataset curation. RGD version 2.0, released in June 2001, includes curated data on rat genes, quantitative trait loci (QTL), microsatellite markers and rat strains used in genetic and genomic research. VCMap, a dynamic sequence-based homology tool was introduced, and allows researchers of rat, mouse and human to view mapped genes and sequences and their locations in the other two organisms, an essential tool for comparative genomics. In addition, RGD provides tools for gene prediction, radiation hybrid mapping, polymorphic marker selection and more. Future developments will include the introduction of disease-based curation expanding the curated information to cover popular disease systems studied in the rat. This will be integrated with the emerging rat genomic sequence and annotation pipelines to provide a high-quality disease-centric resource, applicable to human and mouse via comparative tools such as VCMap. RGD has a defined community outreach focus with a Visiting Scientist program and the Rat Community Forum, a web-based forum for rat researchers and others interested in using the rat as an experimental model. Thus, RGD is not only a valuable resource for those working with the rat but also for researchers in other model organisms wishing to harness the existing genetic and physiological data available in the rat to complement their own work.

Animals↗

PubMed2003

WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures.

WebFEATURE (http://feature.stanford.edu/webfeature/) is a web-accessible structural analysis tool that allows users to scan query structures for functional sites in both proteins and nucleic acids. WebFEATURE is the public interface to the scanning algorithm of the FEATURE package, a supervised learning algorithm for creating and identifying 3D, physicochemical motifs in molecular structures. Given an input structure or Protein Data Bank identifier (PDB ID), and a statistical model of a functional site, WebFEATURE will return rank-scored 'hits' in 3D space that identify regions in the structure where similar distributions of physicochemical properties occur relative to the site model. Users can visualize and interactively manipulate scored hits and the query structure in web browsers that support the Chime plug-in. Alternatively, results can be downloaded and visualized through other freely available molecular modeling tools, like RasMol, PyMOL and Chimera. A major application of WebFEATURE is in rapid annotation of function to structures in the context of structural genomics.

Algorithms↗

PubMed2006

A systematic approach to infer biological relevance and biases of gene network structures.

The development of high-throughput technologies has generated the need for bioinformatics approaches to assess the biological relevance of gene networks. Although several tools have been proposed for analysing the enrichment of functional categories in a set of genes, none of them is suitable for evaluating the biological relevance of the gene network. We propose a procedure and develop a web-based resource (BIOREL) to estimate the functional bias (biological relevance) of any given genetic network by integrating different sources of biological information. The weights of the edges in the network may be either binary or continuous. These essential features make our web tool unique among many similar services. BIOREL provides standardized estimations of the network biases extracted from independent data. By the analyses of real data we demonstrate that the potential application of BIOREL ranges from various benchmarking purposes to systematic analysis of the network biology.

Computational Biology↗

PubMedDate not supplied

Finding the Path: a World Wide Web-based guide for imaging evaluation of patients in the emergency department.

Finding the Path is a problem-based World Wide Web resource that provides algorithms for imaging evaluation of emergency department patients. This module is designed to guide physicians in the efficient use of diagnostic imaging modalities and their appropriate application to emergency department practice. The module is composed of interactive case studies that can be accessed either by diagnoses or as unknowns. Each case study provides a brief clinical history accompanied by pertinent physical and laboratory findings. Users are asked to choose the most appropriate and cost-effective diagnostic imaging study and receive feedback on their choice. Associated images, findings, and a brief discussion of the diagnosis are displayed. Each case is followed by an algorithm aimed at promoting efficient and cost-effective use of imaging modalities. In addition to its value in clinical practice, the database is a useful radiologic teaching tool for residents and medical students. The module is being used at a major university as part of the new curriculum for radiologic education.

Algorithms↗

PubMedDate not supplied

Sustaining Oncology Studies--SOS: information and support for training, research and exploitation in cancer and related biomedical disciplines.

This paper outlines the development of the Sustaining Oncology Studies Information Resources (SOS Europe), a multimedia World Wide Web (WWW) prototype providing support to experimental and clinical cancer researchers, general practitioners, industry personnel, and university students in the field of oncology in Europe and Italy. The system utilizes applications developed for the WWW and is designed in the most easily understandable approaches possible. The prototype now structures oncology-related information available on the Internet and also places resources maintained locally at users' disposal. The system utilizes a WWW browser as a design platform and HTML to build its Home and subpages and to create hyperlinks to internal and external resources.

Computer Communication Networks↗

PubMed1980

Local inactivation of funnel-web spider (Atrax robustus) venom by first-aid measures: potentially lifesaving part of treatment.

Venom of the male Sydney funnel-web spider was injected subcutaneously into the limbs of monkeys (Macaca fascicularis), and the central movement of venom was delayed by first-aid treatment. This treatment consisted of the application of firm pressure over the site of injection and immobilization of the limb. It was found that quantities of venom as high as 2 mg were inactivated when the first-aid procedures were maintained for 24 hours. Over a six-hour period, 0.5 mg of venom could be inactivated. Since the amount of venom injected by the spider into a human victim is unlikely to exceed 0.2 mg, these findings have immediate application both to the first aid and to actual medical management of human victims.

Animals↗

PubMed2000

An "infobutton" for enabling patients to interpret on-line Pap smear reports.

We describe the development of a prototype application that would allow patients with little or no medical background to understand their Pap smear reports. This information button, or "infobutton", is attached to on-line text reports describing Pap smear results present in a medical record system intended for patient access (PatCIS). The infobutton application generates an explanation of terms present in the report and a list of questions related to the terms in the report, which link to publicly accessible resources on the Web.

Data Display↗

PubMedDate not supplied

Women's health: pregnancy and childbirth. Progress on key issues in maternal nutrition.

Great progress on key issues in maternal nutrition has been made in the past few years, mainly because of the legislative requirements of the U.S. Department of Agriculture's Special Supplemental Food Program for Women, Infants, and Children (WIC Program). These advances are most timely because of the general recognition that, in this period of finite resources, we will need to make optimal use of resources such as the food package, nutrition education, and health services that together make up the WIC Program benefits. Major progress has been made in the following critical areas: (a) agreement on nutritional risk criteria; (b) identification of dietary risk factors; (c) increased availability of a variety of computer-assisted techniques for collecting, managing, and analyzing dietary intakes on large numbers of patients; and (d) recognition of the need for and availability of a variety of alternative dietary standards in the provision of overall services to pregnant women. Of even greater importance is the recognition that we can no longer treat nutrition as a single variable, independent of the many other forces that together influence the course and outcome of a pregnancy. Rather, we recognize that there is a seamless web of influences, all of which need to be taken into account in attempts to provide for the needs of pregnant women at risk of poor pregnancy outcomes. The timely application of all of these advances will greatly facilitate a more efficient and effective use of resources such as are provided by the WIC Program. They will also provide both the patients and their health care providers with more realistic expectations of what might be accomplished towards improving the outcomes of pregnancies at nutritional risk.

Female↗

PubMed2006

Development of nursing care quality improvement system on website in Japan.

A model for measuring the quality of nursing care has been developed in Japan since 1993 by Katada. Then a self evaluation model was developed in 2002 by Abe et al. This model consisted of three dimensions: structure, process, and outcome. Each dimension was constructed from measurements of six domains which applicants categorized previously, such as "understanding individuality", "patient empowerment", "family care", "direct care", "medical team coordination", and "incident prevention" In this study, it has been developed and posted on a web site for inspection and examined for its usability.

Humans↗

PubMed2005

A novel application of the MIRC repository in medical education.

Medical students on the radiology elective in our institution create electronic presentations to present to each other as part of the requirements for the rotation. Access was given to previous students' presentations via the web-based system, Medical Imaging Resource Center (MIRC) project, created and supported by the Radiological Society of North America (RSNA). RadPix Power 2 MIRC (Weadock Software, LLC, Ann Arbor, MI) software converted the Microsoft PowerPoint (Redmond, WA) presentations to a MIRC-compatible format. The textual information on each slide is searchable across the entire MIRC database. Future students will be able to benefit from the work of their predecessors.

Computer-Assisted Instruction↗