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At least 433 records · Page 24Linked to original sources

The Online London Dysmorphology Database.

A prototype of the Online London Dysmorphology Database is now available for testing purposes. In this paper we describe the new online version of the London Dysmorphology Database (LDDB), which is accessible via the World-Wide Web. The system has been developed primarily to address the information lag associated with the stand-alone version of LDDB (currently 3-15 months) and therefore provides access to the latest data from the master database that resides on a web server. An additional benefit is that, because the Online LDDB is a web-based resource, it will be available to users of both Macintosh and Unix computers as well as PC users.

Animals↗

Visualizing sequence similarity of protein families.

Classification of proteins into families is one of the main goals of functional analysis. Proteins are usually assigned to a family on the basis of the presence of family-specific patterns, domains, or structural elements. Whereas proteins belonging to the same family are generally similar to each other, the extent of similarity varies widely across families. Some families are characterized by short, well-defined motifs, whereas others contain longer, less-specific motifs. We present a simple method for visualizing such differences. We applied our method to the Arabidopsis thaliana families listed at The Arabidopsis Information Resource (TAIR) Web site and for 76% of the nontrivial families (families with more than one member), our method identifies simple similarity measures that are necessary and sufficient to cluster members of the family together. Our visualization method can be used as part of an annotation pipeline to identify potentially incorrectly defined families. We also describe how our method can be extended to identify novel families and to assign unclassified proteins into known families.

Arabidopsis Proteins↗

Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database.

We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, the functional Dictionary of Homologous Superfamilies (DHS) and PDBsum. Currently Gene3D provides annotation for 36 complete genomes (two eukaryotes, six archaea, and 28 bacteria). On average, between 30% and 40% of the genes of a given genome can be structurally annotated. Matches to structural domains are found using the profile-based method (PSI-BLAST). and a novel protocol, DRange, is used to resolve conflicts in matches involving different homologous superfamilies.

Animals↗

GeneDesign: rapid, automated design of multikilobase synthetic genes.

Modern molecular biology has brought many new tools to the geneticist as well as an exponentially expanding database of genomes and new genes for study. Of particular use in the analysis of these genes is the synthetic gene, a nucleotide sequence designed to the specifications of the investigator. Typically, synthetic genes encode the same product as the gene of interest, but the synthetic nucleotide sequence for that protein may contain modifications affecting expression or base composition. Other desirable changes typically involve the revision of restriction sites. Designing synthetic genes by hand is a time-consuming and error-prone process that may involve several computer programs. We have developed a tools environment that combines many modules to provide a platform for rapid synthetic gene design for multikilobase sequences. We have used GeneDesign to successfully design a synthetic Ty1 element and a large variety of other synthetic sequences. GeneDesign has been implemented as a publicly accessible Web-based resource and can be found at http://slam.bs.jhmi.edu/gd.

Genetic Engineering↗

The Biological Macromolecule Crystallization Database: crystallization procedures and strategies.

The Biological Macromolecule Crystallization Database (BMCD) archives crystallization data from published reports for all forms of biological macromolecules that have produced crystals suitable for X-ray diffraction studies. The information includes the crystallization conditions, crystal data, comments about the crystallization procedure and information on the biological macromolecule or biological macromolecule complex. Crystallization procedures, including fast screens and more general procedures, can be developed effectively using this web-based resource (http://wwwbmcd.nist.gov:8080/bmcd/bmcd.html).

Crystallization↗

Using the worldwide web to improve children's pain care.

AIM: This paper describes a three-year project, the aims of which were to disseminate information regarding the assessment and management of children's pain, to reach consensus on the essential elements of pain assessment for children and to track nurses' perceived changes in pain assessment and management practices in hospital settings over time. BACKGROUND: Despite the availability of research, guidelines and standards, paediatric nurses inconsistently practice evidence-based pain management. PROJECT METHODS: Nurses attending the 5th International Symposium on Paediatric Pain were invited to a workshop to discuss best practices and consider ways to share information regarding the assessment and management of children's pain. A website was designed and participants provided hospital guidelines, exchanged information via the Internet and completed periodic surveys. CONCLUSION: Web-based resources were positively received. Consensus regarding the essential elements of pain management was achieved, but nurses identified organizational and resource restraints as barriers to achieving best practices. Surveys identified perceived increases in some hospital and ward level resources and activities to improve children's pain care. Sharing of information related to children's pain management and benchmarking of practice should be encouraged. Consensus building and networking may facilitate change, but organizational commitment is also required for successful implementation of new practices.

Consensus↗

The injured child.

Pre-hospital immediate care for seriously injured children is rarely required, but when it is, the response must be prompt and effective. The key to an effective and confident approach to injured children lies in understanding the age related anatomical and physiological differences between adults and children. These differences are most exaggerated in the first few years of life and excellent training courses and materials are available to help practitioners develop their confidence and skills in this age group. An easy to use length based aide memoire and a set of equipment packed according to size are essential to ensure safe management in the pre-hospital environment. Care of the seriously ill child, emergency childbirth and neonatal resuscitation are beyond the scope of this article. Nonetheless, pre-hospital practitioners should develop an understanding of assessment of ill children and normal delivery and be prepared to assist with emergency childbirth and neonatal resuscitation. Excellent educational material, courses and web based resources are available to achieve this (54). This is the sixth article in the add on series in pre-hospital care. The series is edited by Maj R Mackenzie. Maj RC Sutcliffe is a general practitioner and regimental medical officer. Maj R Mackenzie is a Specialist Registrar in Accident and Emergency Medicine and an immediate care doctor. While every effort has been made to ensure correct drug dosages are quoted, readers should always check these before use.

Child↗

Database for renal collecting duct regulatory and transporter proteins.

The mammalian kidney collecting duct plays an important role in the fine regulation of Na, K, water, and acid-base balance. Functional genomic and proteomic studies of the kidney offer new opportunities in the understanding of renal physiology and pathophysiology, and the collecting duct is an appropriate target tissue because of the relative simplicity of its cells and the ease of isolating or culturing large numbers of collecting duct cells. Study of the collecting duct includes assessment of gene expression and protein regulation and abundance. For example, DNA and protein microarrays can be used to quantitate gene expression and protein regulation and abundance under varying physiological conditions. An Internet-accessible database has been devised for major collecting duct proteins involved in transport and regulation of cellular processes. The individual proteins included in this database are those culled from literature searches and from previously published studies involving cDNA arrays and serial analysis of gene expression (SAGE). Design of microarray targets for the study of kidney collecting duct tissues is facilitated by the database, which includes links to curated base pair and amino acid sequence data, relevant literature, and related databases. Use of the database is illustrated by a search for water channel proteins, aquaporins, and by a subsequent search for vasopressin receptors. Links are shown to the literature and to sequence data for human, rat, and mouse, as well as to relevant web-based resources. Extension of the database is dynamic and is done through a maintenance interface. This permits creation of new categories, updating of existing entries, and addition of new ones.

Animals↗

Gene homology resources on the World Wide Web.

As the amount of information available to biologists increases exponentially, data analysis becomes progressively more challenging. Sequence homology has been a traditional tool in the researchers' armamentarium; it is a very versatile instrument and can be employed to assist in numerous tasks, from establishing the function of a gene to determination of the evolutionary development of an organism. Consequently, numerous specialized tools have been established in the public domain (most commonly, the World Wide Web) to help investigators use sequence homology in their research. These homology databases differ both in techniques they use to compare sequences as well as in the size of the unit of analysis, which can be the whole gene, a domain, or a motif. In this paper, we aim to present a systematic review of the inner details of the most commonly used databases as well as to offer guidelines for their use.

Animals↗

Assessing the ACGME Competencies in Psychiatry Training programs.

In 2000, the Accreditation Council of Graduate Medical Education (ACGME) laid out a definition of competence that included six specific areas of focus: patient care (including clinical reasoning), medical knowledge, practice-based learning and improvement, interpersonal and communication skills, professionalism, and systems-based practice. The ACGME's intention was to mandate increasingly reliable and valid assessment measures to be used by all training programs over the next decade, with the goal of providing "more credible, accurate, reliable and useful educational outcome data." In this article, the authors will review definitions of competency according to the new ACGME standards and examine the assessment tools currently available, including global evaluations, 360-degree evaluations, checklists, standardized examinations and direct observations. The authors will provide an overview of critical considerations in different assessment methods, including timing, psychometric properties, benchmarks, and feedback. Finally, the authors will discuss the relevant literature concerning the strengths and weaknesses of these various assessment tools. Throughout, the authors will comment on the applicability of the literature on assessment to the field of psychiatry and consider directions for competency assessment within and beyond psychiatric training. Following the paper is an annotated bibliography of the literature for those wishing to explore this topic more deeply and a list of web-based resources that may be used by those wishing to access available instruments.

Accreditation↗

Implementing evidence-based practices for persons with severe mental illnesses.

Extensive empirical research, summarized in several reviews and codified in practice guidelines, recommendations, and algorithms, demonstrates that several pharmacological and psychosocial interventions are effective in improving the lives of persons with severe mental illnesses. Yet the practices validated by research are not widely offered in routine mental health practice settings. As part of an effort to promote the implementation of evidence-based practice, the authors summarize perspectives on how best to change and sustain effective practice from the research literature and from the experiences of administrators, clinicians, family advocates, and services researchers. They describe an implementation plan for evidence-based practices based on the use of toolkits to promote the consistent delivery of such practices. The toolkits will include integrated written material, Web-based resources, training experiences, and consultation opportunities. Special materials will address the concerns of mental health authorities (funders), administrators of provider organizations, clinicians, and consumers and their families.

Community Mental Health Services↗

K-SPMM: a database of murine spermatogenic promoters modules & motifs.

BACKGROUND: Understanding the regulatory processes that coordinate the cascade of gene expression leading to male gamete development has proven challenging. Research has been hindered in part by an incomplete picture of the regulatory elements that are both characteristic of and distinctive to the broad population of spermatogenically expressed genes. DESCRIPTION: K-SPMM, a database of murine Spermatogenic Promoters Modules and Motifs, has been developed as a web-based resource for the comparative analysis of promoter regions and their constituent elements in developing male germ cells. The system contains data on 7,551 genes and 11,715 putative promoter regions in Sertoli cells, spermatogonia, spermatocytes and spermatids. K-SPMM provides a detailed portrait of promoter site components, ranging from broad distributions of transcription factor binding sites to graphical illustrations of dimeric modules with respect to individual transcription start sites. Binding sites are identified through their similarities to position weight matrices catalogued in either the JASPAR or the TRANSFAC transcription factor archives. A flexible search function allows sub-populations of promoters to be identified on the basis of their presence in any of the four cell-types, their association with a list of genes or their component transcription-factor families. CONCLUSION: This system can now be used independently or in conjunction with other databases of gene expression as a powerful aid to research networks of co-regulation. We illustrate this with respect to the spermiogenically active protamine locus in which binding sites are predicted that align well with biologically foot-printed protein binding domains. AVAILABILITY: http://klab.med.wayne.edu/kspmm/

Amino Acid Motifs↗

iHAP--integrated haplotype analysis pipeline for characterizing the haplotype structure of genes.

BACKGROUND: The advent of genotype data from large-scale efforts that catalog the genetic variants of different populations have given rise to new avenues for multifactorial disease association studies. Recent work shows that genotype data from the International HapMap Project have a high degree of transferability to the wider population. This implies that the design of genotyping studies on local populations may be facilitated through inferences drawn from information contained in HapMap populations. RESULTS: To facilitate analysis of HapMap data for characterizing the haplotype structure of genes or any chromosomal regions, we have developed an integrated web-based resource, iHAP. In addition to incorporating genotype and haplotype data from the International HapMap Project and gene information from the UCSC Genome Browser Database, iHAP also provides capabilities for inferring haplotype blocks and selecting tag SNPs that are representative of haplotype patterns. These include block partitioning algorithms, block definitions, tag SNP definitions, as well as SNPs to be "force included" as tags. Based on the parameters defined at the input stage, iHAP performs on-the-fly analysis and displays the result graphically as a webpage. To facilitate analysis, intermediate and final result files can be downloaded. CONCLUSION: The iHAP resource, available at http://ihap.bii.a-star.edu.sg, provides a convenient yet flexible approach for the user community to analyze HapMap data and identify candidate targets for genotyping studies.

Algorithms↗

In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

BACKGROUND: Abnormalities of pre-mRNA splicing are increasingly recognized as an important mechanism through which gene mutations cause disease. However, apart from the mutations in the donor and acceptor sites, the effects on splicing of other sequence variations are difficult to predict. Loosely defined exonic and intronic sequences have been shown to affect splicing efficiency by means of silencing and enhancement mechanisms. Thus, nucleotide substitutions in these sequences can induce aberrant splicing. Web-based resources have recently been developed to facilitate the identification of nucleotide changes that could alter splicing. However, computer predictions do not always correlate with in vivo splicing defects. The issue of unclassified variants in cancer predisposing genes is very important both for the correct ascertainment of cancer risk and for the understanding of the basic mechanisms of cancer gene function and regulation. Therefore we aimed to verify how predictions that can be drawn from in silico analysis correlate with results obtained in an in vivo splicing assay. RESULTS: We analysed 99 hMLH1 and hMSH2 missense mutations with six different algorithms. Transfection of three different cell lines with 20 missense mutations, showed that a minority of them lead to defective splicing. Moreover, we observed that some exons and some mutations show cell-specific differences in the frequency of exon inclusion. CONCLUSION: Our results suggest that the available algorithms, while potentially helpful in identifying splicing modulators especially when they are located in weakly defined exons, do not always correspond to an obvious modification of the splicing pattern. Thus caution must be used in assessing the pathogenicity of a missense or silent mutation with prediction programs. The variations observed in the splicing proficiency in three different cell lines suggest that nucleotide changes may dictate alternative splice site selection in a tissue-specific manner contributing to the widely observed phenotypic variability in inherited cancers.

Adaptor Proteins, Signal Transducing↗

NIDDK data repository: a central collection of clinical trial data.

BACKGROUND: The National Institute of Diabetes and Digestive and Kidney Diseases have established central repositories for the collection of DNA, biological samples, and clinical data to be catalogued at a single site. Here we present an overview of the site which stores the clinical data and links to biospecimens. DESCRIPTION: The NIDDK Data repository is a web-enabled resource cataloguing clinical trial data and supporting information from NIDDK supported studies. The Data Repository allows for the co-location of multiple electronic datasets that were created as part of clinical investigations. The Data Repository does not serve the role of a Data Coordinating Center, but rather as a warehouse for the clinical findings once the trials have been completed. Because both biological and genetic samples are collected from many of the studies, a data management system for the cataloguing and retrieval of samples was developed. CONCLUSION: The Data Repository provides a unique resource for researchers in the clinical areas supported by NIDDK. In addition to providing a warehouse of data, Data Repository staff work with the users to educate them on the datasets as well as assist them in the acquisition of multiple data sets for cross-study analysis. Unlike the majority of biological databases, the Data Repository acts both as a catalogue for data, biosamples, and genetic materials and as a central processing point for the requests for all biospecimens. Due to regulations on the use of clinical data, the ultimate release of that data is governed under NIDDK data release policies. The Data Repository serves as the conduit for such requests.

Access to Information↗

Locating grey literature on communication disorders.

This article provides an overview of selected Web-based resources containing grey literature in the area of communication disorders. It is geared to practitioners, researchers, students, and consumers seeking reliable, freely available scientific information. Grey (or gray) literature has been defined as "that which is produced on all levels of government, academics, business, and industry in print and electronic formats, but which is not controlled by commercial publishers."1 This paper reviews various general reference sources potentially containing grey literature on communication disorders. This review includes identification of the methods specialists in this field use to obtain this valuable, yet often overlooked, literature. Access points and search tools for identifying grey literature on communication disorders are recommended. Commercial databases containing grey literature are not included. Conclusions presented in this article are considered complementary to traditionally published information resources on communication disorders, such as scholarly journals, online databases, etc.

Academic Medical Centers↗

Exercise information resources on the World Wide Web.

Health professionals and members of the public are often interested in locating exercise information on the World Wide Web (the Web). There is a large amount of information available on the Web; however, the challenge for all people is to identify the high quality information that can be depended upon. Much of the quality exercise information on the Web is hidden within sites of reputable organizations concerned with exercise and health. This article examines several categories of commonly needed exercise related information. For each category, a few high quality sources of exercise information are listed. Combined, these Web sites provide an excellent and extensive body of knowledge for a person who is not experienced with exercise and wants to get started learning, or for a person with a moderate level of experience and knowledge who wants to learn more.

Exercise↗

Computer software to find genes in plant genomic DNA.

Gene finding is the most important phase of genome annotation. Eukaryotic genomes contain thousands of protein coding genes, and computational gene prediction would rapidly increase the pace of experimental confirmation of expressed genes at the bench. The purpose of this chapter is to discuss the use of different computer programs that identify protein-coding genes in large genomic sequences. We describe most commonly used gene prediction programs that are available on the World Wide Web and demonstrate the use of some of these programs by an example. We provide a list of these programs along with their. Web uniform resource locators (URLs) and suggest guidelines for successful gene finding.

Arabidopsis↗