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At least 235 records · Page 13Linked to original sources
PubMed2006

SNPs3D: candidate gene and SNP selection for association studies.

BACKGROUND: The relationship between disease susceptibility and genetic variation is complex, and many different types of data are relevant. We describe a web resource and database that provides and integrates as much information as possible on disease/gene relationships at the molecular level. DESCRIPTION: The resource http://www.SNPs3D.org has three primary modules. One module identifies which genes are candidates for involvement in a specified disease. A second module provides information about the relationships between sets of candidate genes. The third module analyzes the likely impact of non-synonymous SNPs on protein function. Disease/candidate gene relationships and gene-gene relationships are derived from the literature using simple but effective text profiling. SNP/protein function relationships are derived by two methods, one using principles of protein structure and stability, the other based on sequence conservation. Entries for each gene include a number of links to other data, such as expression profiles, pathway context, mouse knockout information and papers. Gene-gene interactions are presented in an interactive graphical interface, providing rapid access to the underlying information, as well as convenient navigation through the network. Use of the resource is illustrated with aspects of the inflammatory response and hypertension. CONCLUSION: The combination of SNP impact analysis, a knowledge based network of gene relationships and candidate genes, and access to a wide range of data and literature allow a user to quickly assimilate available information, and so develop models of gene-pathway-disease interaction.

Databases, Genetic↗
PubMed2003

Does anybody read "evidence-based" articles?

BACKGROUND: The electronic version of the British Medical Journal (eBMJ) has a unique feature in that it provides an electronic record of the number of times an article has been viewed ("hits") in the week after its publication. We sought to compare the relative popularity of primary research and "evidence-based" papers against that of narrative reviews and editorials. We surveyed four broad groupings of articles in 2001: Editorials, Clinical Reviews (which are narrative reviews), Education and Debate, and Papers (which are original research articles and systematic reviews). Clinical Reviews were the most frequently viewed articles, with an average of 4148 hits per article, while Papers were less popular (average of 1168 hits per article). Systematic reviews (23 articles, average of 1190 hits per article) were visited far less often than narrative reviews. Editorials (average of 2537 hits per article) were viewed much more frequently than Papers, even where the editorial was written as an accompanying piece with a direct link to the paper. DISCUSSION: Narrative reviews and editorials are accessed more frequently than primary research papers or systematic reviews in the first week after their publication. These findings may disappoint those who believe that it is important for readers to critically appraise the primary research data. Although the technical quality of journal articles may have been helped by recommendations on structured reporting, the readability of such articles has received little attention. Authors and journal editors must take steps to make research articles and systematic reviews more attractive to readers. This may involve using simpler language, as well as innovative use of web resources to produce shorter, snappier papers, with the methodological or technical details made available elsewhere. CONCLUSION: Primary research and "evidence-based" papers seem to be less attractive to readers than narrative reviews and editorials in the first week after publication. Authors and editors should try to improve the early appeal of primary research papers.

Evidence-Based Medicine↗
PubMed2006

PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification.

The Berkeley Phylogenomics Group presents PhyloFacts, a structural phylogenomic encyclopedia containing almost 10,000 'books' for protein families and domains, with pre-calculated structural, functional and evolutionary analyses. PhyloFacts enables biologists to avoid the systematic errors associated with function prediction by homology through the integration of a variety of experimental data and bioinformatics methods in an evolutionary framework. Users can submit sequences for classification to families and functional subfamilies. PhyloFacts is available as a worldwide web resource from http://phylogenomics.berkeley.edu/phylofacts.

Animals↗
PubMed2005

Information literacy in biology education: an example from an advanced cell biology course.

Information literacy skills are critically important for the undergraduate biology student. The ability to find, understand, evaluate, and use information, whether from the scientific literature or from Web resources, is essential for a good understanding of a topic and for the conduct of research. A project in which students receive information literacy instruction and then proceed to select, update, and write about a current research topic in an upper-level cell biology course is described. Students research the chosen topic using paper and electronic resources, generate a list of relevant articles, prepare abstracts based on papers read, and, finally, prepare a "state-of-the-art" paper on the topic. This approach, which extends over most of one semester, has resulted in a number of well-researched and well-written papers that incorporate some of the latest research in cell biology. The steps in this project have also led to students who are prepared to address future projects on new and complex topics. The project is part of an undergraduate course in cell biology, but parts of the assignments can be modified to fit a variety of subject areas and levels.

Abstracting and Indexing↗
PubMed2004

A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge.

OBJECTIVE: Biomedical databases summarize current scientific knowledge, but they generally require years of laborious curation effort to build, focusing on identifying pertinent literature and data in the voluminous biomedical literature. It is difficult to manually extract useful information embedded in the large volumes of literature, and automated intelligent text analysis tools are becoming increasingly essential to assist in these curation activities. The goal of the authors was to develop an automated method to identify articles in Medline citations that contain pharmacogenetics data pertaining to gene-drug relationships. DESIGN: The authors built and evaluated several candidate statistical models that characterize pharmacogenetics articles in terms of word usage and the profile of Medical Subject Headings (MeSH) used in those articles. The best-performing model was used to scan the entire Medline article database (11 million articles) to identify candidate pharmacogenetics articles. RESULTS: A sampling of the articles identified from scanning Medline was reviewed by a pharmacologist to assess the precision of the method. The authors' approach identified 4,892 pharmacogenetics articles in the literature with 92% precision. Their automated method took a fraction of the time to acquire these articles compared with the time expected to be taken to accumulate them manually. The authors have built a Web resource (http://pharmdemo.stanford.edu/pharmdb/main.spy) to provide access to their results. CONCLUSION: A statistical classification approach can screen the primary literature to pharmacogenetics articles with high precision. Such methods may assist curators in acquiring pertinent literature in building biomedical databases.

Bayes Theorem↗
PubMed2001

Patients' rights on the World Wide Web.

Managed care reform, commonly referred to as "patients' rights" legislation, has become a hot topic. Many groups, including consumers, health care professionals, employers, managed care organizations, political parties, and government agencies, have strong opinions about measures that should be taken and what the outcomes of these measures might be. Those investigating this multidisciplinary topic will want to examine health care administration, ethics, health services research, and political science sources. Web resources covered in this article include: clearinghouses; government agencies; federal legislative and legal sites; and home pages of professional and trade associations, policy research institutes, and consumer advocacy organizations.

Health Care Sector↗
PubMed2005

Using education to promote research dissemination in nursing.

In order to maintain the highest standards of care, nurses need to be aware of the most recent and relevant research and use this to inform their practice. However, this is often difficult because of both the limited time available in which to access research and the need for advanced critical appraisal skills. Further, given the overload of complex research information, nurses may be overwhelmed by the extent of available research. This paper describes a unique approach, the Web Resource Appraisal Process (WRAP), for integrating research and education by directly engaging nurses undertaking postgraduate studies in the review of existing research as it is applied to the contemporary workplace. In so doing, experienced nurses investigate the application of research to practice by actively engaging in research dissemination, communication, and education. By engaging in this process, nurses generate new knowledge based on the integration of current research with their practice experience, while simultaneously gaining the benefits of experiential learning.

Communication↗
PubMedDate not supplied

Developing and evaluating patient education materials.

Nurses should be involved in all aspects of patient education, including the development of print and web resources, but most nurses have not been educated in how to develop these resources. This article discusses the rationale for nurse involvement, describes guidelines for evaluating existing material for credibility and readability, and provides recommendations for rewriting material at an easier-to-read level.

Educational Status↗
PubMed2000

High volume medical web sites.

In 1998, 22 million individuals reported surfing the web for medical information, and this number will increase to over 30 million by 2000. Fifteen of the highest volume medical web sites are described in this paper. Sponsorship and/or ownership of the fifteen sites varied. The government sponsors one, and some are the products of well-known educational institutions. One site is supported by a consumer health organization, and the American Medical Association was in the top 15. However, the most common owners are commercial, for-profit businesses. Attributes of the ideal site were categorized, and include a robust privacy and disclosure statement with an emphasis on education and an appropriate role for advertising. The covering of Complementary and Alternative Medicine (CAM) should be in a balanced and unbiased manner. There has to be an emphasis on knowledge based evidence as opposed to testimonials, and sources should be timely and reviewed. Bibliographies of authors need to be available. Hyperlinking to other web resources is valuable, as even the largest of sites cannot come close to covering all of medicine.

Confidentiality↗
PubMed2002

[Oncologic gynecology and the Internet].

The strategy of World Wide Web searching for medical sites was presented in this article. The "deep web" and "surface web" resources were searched. The 10 best sites connected with the gynecological oncology, according to authors' opinion, were presented.

Databases, Bibliographic↗
PubMed2003

IMGT, the international ImMunoGeneTics information system, http://imgt.cines.fr: the reference in immunoinformatics.

IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), is a high quality integrated information system specializing in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) and related proteins of the immune system of human and other vertebrates, created in 1989, by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM), at the Université Montpellier II, CNRS, Montpellier, France. IMGT is the global reference in immunogenetics and immunoinformatics and provides a common access to standardized data which include nucleotide and protein sequences, oligonucleotide primers, gene maps, genetic polymorphisms, specificities, 2D and 3D structures. IMGT includes three sequence databases (IMGT/LIGM-DB, IMGT/MHC-DB hosted at EBI, IMGT/PRIMER-DB), one genome database (IMGT/GENE-DB), one 3D structure database (IMGT/3Dstructure-DB), Web resources comprising 8000 HTML pages ("IMGT Marie-Paule page") and interactive tools for sequence (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/Allele-Align, IMGT/PhyloGene) and genome (IMGT/GeneSearch, IMGT/GeneView, IMGT/LocusView) analysis. IMGT data are expertly annotated according to the rules of the IMGT Scientific chart, based on the IMGT-ONTOLOGY concepts. IMGT tools are particularly useful for the analysis of the IG and TR repertoires in physiological normal and pathological situations. IMGT has important applications in medical research (repertoire analysis in autoimmune diseases, AIDS, leukemias, lymphomas, myelomas), biotechnology related to antibody engineering (phage displays, combinatorial libraries) and therapeutic approaches (graft, immunotherapy). IMGT is freely available at http://imgt.cines.fr.

Animals↗
PubMed2004

Evaluation of parameters influencing S values in mouse dosimetry.

UNLABELLED: Clinical radionuclide therapy studies are commonly preceded by studies with small animals. Reliable evaluation of therapeutic efficacy must be based on accurate dosimetry. This study was performed to evaluate the influence of the mass of organs, the shape of organs, and the distances between organs on S values for mice. METHODS: A voxel-based version of a geometric model of a mouse was developed for input in our Monte Carlo program based on EGS4. Simulations were made for each source organ separately to resolve the S values for each organ. For verification purposes, S values were calculated for spheres of different masses and compared with the S values in the MIRDOSE3.1 software and with the S values on the Radiation Dose Assessment Resource Web site. The variation in the mass of the organs was determined from dissected mice. The influence of the shape of an organ was investigated by successive elongation of a sphere into spheroids with a constant mass. The right kidney was moved in the phantom of the mouse to evaluate the effect of organ distances on S values. The absorbed fractions for the mouse model presented here were compared with the results from some previously published models. The radionuclides used were (90)Y, (131)I, (111)In, and (99m)Tc. RESULTS: The results showed that the organ mass for one animal can differ by up to 33% from the mean mass. If linear interpolation from S value tables is used to obtain an S value for the specific mass of an organ, then the S value can differ by up to 80% from its true value. The corresponding deviation obtained by scaling according to mass is 20%. The shape of an organ was found to be the least important parameter for the S value. The cross-absorbed S value is strongly dependent on the geometry and the emitted radiation. For example, a 9.2-mm movement of the kidney can cause the S value from the liver to the right kidney to decrease to 0.05% of its original value for (90)Y. CONCLUSION: We conclude that the mass and the shape of organs and their locations relative to each other have considerable effects on mouse dosimetry.

Algorithms↗
PubMed2005

T cell receptor/peptide/MHC molecular characterization and standardized pMHC contact sites in IMGT/3Dstructure-DB.

One of the key elements in the adaptive immune response is the presentation of peptides by the major histocompatibility complex (MHC) to the T cell receptors (TR) at the surface of T cells. The characterization of the TR/peptide/MHC trimolecular complexes (TR/pMHC) is crucial to the fields of immunology, vaccination and immunotherapy. In order to facilitate data comparison and cross-referencing between experiments from different laboratories whatever the receptor, the chain type, the domain, or the species, IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), has developed IMGT-ONTOLOGY, the first ontology in immunogenetics and immunoinformatics. In IMGT/3Dstructure-DB, the IMGT three-dimensional structure database, TR/pMHC molecular characterization and pMHC contact analysis are made according to the IMGT Scientific chart rules, based on the IMGT-ONTOLOGY concepts. IMGT/3Dstructure-DB provides the standardized IMGT gene and allele names (CLASSIFICATION), the standardized IMGT labels (DESCRIPTION) and the IMGT unique numbering (NUMEROTATION). As the IMGT structural unit is the domain, amino acids at conserved positions always have the same number in the IMGT databases, tools and Web resources. For the TR alpha and beta chains, the amino acids in contact with the peptide/MHC (pMHC) are defined according to the IMGT unique numbering for V-DOMAIN. The MHC cleft that binds the peptide is formed by two groove domains (G-DOMAIN), each one comprising four antiparallel beta strands and one alpha helix. The IMGT unique numbering for G-DOMAIN applies both to the first two domains (G-ALPHA1 and G-ALPHA2) of the MHC class I alpha chain, and to the first domain (G-ALPHA and G-BETA) of the two MHC class II chains, alpha and beta. Based on the IMGT unique numbering, we defined eleven contact sites for the analysis of the pMHC contacts. The TR/pMHC contact description, based on the IMGT numbering, can be queried in the IMGT/StucturalQuery tool, at http://imgt.cines.fr.

Amino Acid Sequence↗
PubMed2005

[Tag primer-nested/ multiplex PCR for detection of Plasmodium falciparum and Plasmodium vivax].

OBJECTIVE: To establish a sensitive, simple to use and low noise nested/multiplex PCR for simultaneously detection of Plasmodium falciparum (Pf) and Plasmodium vivax (P.v). METHODS: The tag primer amplification technique, software Primer Premier 5.0, NCBI-BLAST web resources and the matrix test were used to optimize the nested/multiplex PCR for detection of P.f and P.v with filter paper blood samples taken from malaria patients diagnosed by microscopy, and the results of the optimized nested/multiplex PCR and microscopy were evaluated. RESULTS: The sensitivity of the optimized PCR, determined by the examination of imitative filter paper blood samples, was about 1-2 parasites / microl for P.f and 5-10 parasites / microl for P.v. Primer-dimer and other PCR noise were removed. When 71 field filter paper blood samples taken from microscopically diagnosed patients (24 P.f, 47 P.v) were examined, the concordance between the optimized PCR and microscopy was 875% for Pf and 100% for P.v. CONCLUSION: The nested/multiplex PCR optimized by tag primer amplification technique is simple, with low noise and being able to detect Pf and P.v simultaneously. It is more sensitive in detecting cases with low parasitaemia and more accurate in identifying Plasmodium species than microscopy.

Animals↗
PubMed1996

Integrating DXplain into a clinical information system using the World Wide Web.

The World Wide Web(WWW) offers a cross-platform environment and standard protocols that enable integration of various applications available on the Internet. The authors use the Web to facilitate interaction between their Web-based Clinical Information System and a decision-support system-DXplain, at the Massachusetts General Hospital-using local architecture and Common Gateway Interface programs. The current application translates patients laboratory test results into DXplain's terms to generate diagnostic hypotheses. Two different access methods are utilized for this model; Hypertext Transfer Protocol (HTTP) and TCP/IP function calls. While clinical aspects cannot be evaluated as yet, the model demonstrates the potential of Web-based applications for interaction and integration and how local architecture, with a controlled vocabulary server, can further facilitate such integration. This model serves to demonstrate some of the limitations of the current WWW technology and identifies issues such as control over Web resources and their utilization and liability issues as possible obstacles for further integration.

Computer Communication Networks↗
PubMed2005

T-STAG: resource and web-interface for tissue-specific transcripts and genes.

T-STAG (tissue-specific transcripts and genes) is a resource and web-interface, designated to analyze tissue/tumor-specific expression patterns in human and mouse transcriptomes. It integrates our refined prediction of specific expression patterns both in genes as well as in individual isoforms with man-mouse orthology data. In combination with the features for combining/contrasting the genes expressed in different tissues, T-STAG implicates important biological applications, such as the detection of differentially expressed genes in tumors, the retrieval of orthologs with significant expression in the same tissue etc. Additionally, our refined categorization of expressed sequence tags (ESTs) according to the normalization of cDNA libraries allows searching for putative low-abundant transcripts. The results are tightly linked to our visualization tools, GeneNest (expression patterns of genes) and SpliceNest (gene structure and alternative splicing). The user-friendly interface of T-STAG offers a platform for comprehensive analysis of tissue and/or tumor-specific expression patterns revealed by the EST data. T-STAG is freely accessible at http://tstag.molgen.mpg.de.

Animals↗
PubMed1999

The Missouri Developmental Disability Resource Center: a Web site responding to the critical need for information of parents with a child with a disability.

One of the greatest problems for parents who have a child with a developmental disability is a lack of access to information. Parents have a critical need to learn the specifics of their child's disability, the best treatment practices, and how the broader service delivery system works (Bradley, 1992; Rinck, Calkins, Green, & Stadler, 1986). The Missouri Developmental Disabilities Resource Center Web site [http:/(/)www.moddrc.com] was created as an innovative method of meeting the information needs of this underserved population. Challenges to the adoption of this innovative model are highlighted, and some options for addressing these issues are discussed.

Child, Preschool↗
PubMed2005

Analysis of VH gene sequences using two web-based immunogenetics resources gives different results, but the affinity maturation status of chronic lymphocytic leukaemia clones as assessed from either of the resulting data sets has no prognostic significance.

Some cellular and molecular features of chronic lymphocytic leukaemia (CLL) cells that are associated with prognosis may reflect the context within which their progenitors encountered antigen. It follows that the nature of antigen drive in CLL could influence the clinical course and we were prompted to assess the impact, if any, of affinity maturation (an antigen-driven process) on prognosis. Statistical models for assessing affinity maturation status are typically applied to V(H) gene sequence data analysed using a web-based resource like IMGT or VBASE. Since these resources differ with respect to some key relevant features, we evaluated a cohort of CLL cases by applying statistical models to V(H) data derived from both IMGT and VBASE. Important differences between the resulting data sets became apparent. These resulted from database variance and because IMGT and VBASE define complementarity-determining and framework regions (CDRs, FRs) in different ways. Thus, the numbers of mutations identified and their distribution between CDRs/FRs varied between the data sets for the majority of clones. Consequently, two different but overlapping sets of cases with evidence of affinity maturation were defined. Notwithstanding their differences, no significant associations of affinity maturation status with CD38 expression, p53 functional status or survival were identifiable in either data set.

ADP-ribosyl Cyclase↗