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Chronic fatigue syndrome and fibromyalgia resources on the world wide web: a descriptive journey.

A wealth of information on chronic fatigue syndrome (CFS) and fibromyalgia is available on the World Wide Web for health care providers and patients. These illnesses have overlapping features, and their etiologies remain unknown. Multiple Web sites were reviewed, and selected sites providing useful information were identified. Sites were classified according to their content and target audience and were judged according to suggested standards of Internet publishing. Fifty-eight sites were classified into groups as follows: comprehensive and research Web sites for CFS and fibromyalgia, meetings, clinical trials, literature search services, bibliographies, journal, and CFS and fibromyalgia Web sites for the patient.

Directories as Topic↗

Vaccine and immunization resources on the World Wide Web.

Abundant information regarding immunizations and vaccines is available on the World Wide Web. This report was prepared as a guide to reliable Internet sources for health care providers, researchers, and patients or parents interested in gaining Web-based information on these topics. I describe comprehensive Web sites about immunizations, meetings on immunizations, and clinical trials on vaccines and for journals and publications on vaccines, organizations providing immunization information, and pharmaceutical companies and vaccine manufacturers.

Clinical Trials as Topic↗

LDB2000: sequence-based integrated maps of the human genome.

MOTIVATION: Integrated maps are useful for gene mapping and establishing the relationship between recombination and sequence. In this paper we describe algorithms and their implementation for constructing sequence-based integrated maps of the human chromosomes, which are presented in LDB2000, a web based resource. Gene mapping efforts are now focussing on linkage disequilibrium mapping and extension of the integrated map to represent the extent of linkage disequilibrium in different genomic regions would further increase the utility of these maps. RESULTS: Sequence-based integrated maps have been completed for chromosomes 21 and 22. These maps provide locations for genes and polymorphic markers in sequence and on genetic linkage, radiation hybrid and cytogenetic scales. Single nucleotide polymorphisms associated with genes in the maps are also included and their sequence locations indicated. Related locus information, such as aliases and expression information, can be searched on the WWW site.

Algorithms↗

A bioinformatics analysis of protein tyrosine phosphatases in humans.

Protein tyrosine phosphatases (PTPs) cooperate with protein tyrosine kinases to regulate signal transduction pathways. Genome-wide surveys cataloging protein tyrosine phosphatases in humans have recently been carried out. Here, we present a bioinformatics analysis of protein tyrosine phosphatases in the human genome to examine their domain architecture, alternative splicing and pseudogenes. We present evidence that alternative transcripts exist for 25 out of 35 PTPs analyzed. These alternative transcripts include novel exons; skipped exons as well as cryptic donor/acceptor splice sites. We discovered a novel isoform of PTPN18 based on analysis of expressed sequence tags (ESTs). The deletion of 4 exons in the catalytic domain of the novel isoform may alter the enzymatic activity toward its substrates. We were able to experimentally validate 2 of our novel isoform predictions through RT-PCR. Finally, a user-friendly web-based resource that consolidates the gene and protein annotations for all human protein tyrosine phosphatases has been developed and is freely available at http://ptpr.ibioinformatics.org.

Alternative Splicing↗

Sequence variation and disease in the wake of the draft human genome.

The sequencing phase of the human genome project will soon be over. In its wake, repertoires of sequence polymorphisms among the human population are being sampled and a battery of functional genomics projects, from gene and protein expression studies to whole proteome interaction experiments, are generating vast quantities of data. Now that the data, or the means to generate data, are available it is the application of this information in enhancing our understanding of biology that represents the next formidable challenge. Two prominent issues should be considered. First, existing data must be analysed using the best methods available. The prediction of enzymatic activity for bestrophin, whose gene is mutated in Best macular dystrophy, is described in this review. This is an example of the experimentally testable hypotheses that can result from such detailed and exhaustive analyses. Secondly, the torrents of data from high-throughput studies will need to be made more accessible to all using web-based resources that integrate and digest complementary data types. The internet sites that showcase the human genome sequence are blazing a new trail. Ultimately, the success of genome sequencing and functional genomics will be measured not by the quantity and accuracy of raw data generated, but how rapidly they can be harnessed to span the divide between genotype and phenotype.

Alleles↗

WormBase: network access to the genome and biology of Caenorhabditis elegans.

WormBase (http://www.wormbase.org) is a web-based resource for the Caenorhabditis elegans genome and its biology. It builds upon the existing ACeDB database of the C.elegans genome by providing data curation services, a significantly expanded range of subject areas and a user-friendly front end.

Alternative Splicing↗

Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes.

Nematode.net (www.nematode.net) is a web- accessible resource for investigating gene sequences from nematode genomes. The database is an outgrowth of the parasitic nematode EST project at Washington University's Genome Sequencing Center (GSC), St Louis. A sister project at the University of Edinburgh and the Sanger Institute is also underway. More than 295,000 ESTs have been generated from >30 nematodes other than Caenorhabditis elegans including key parasites of humans, animals and plants. Nematode.net currently provides NemaGene EST cluster consensus sequence, enhanced online BLAST search tools, functional classifications of cluster sequences and comprehensive information concerning the ongoing generation of nematode genome data. The long-term goal of nematode.net is to provide the scientific community with the highest quality sequence information and tools for studying these diverse species.

Animals↗

StellaBase: the Nematostella vectensis Genomics Database.

StellaBase, the Nematostella vectensis Genomics Database, is a web-based resource that will facilitate desktop and bench-top studies of the starlet sea anemone. Nematostella is an emerging model organism that has already proven useful for addressing fundamental questions in developmental evolution and evolutionary genomics. StellaBase allows users to query the assembled Nematostella genome, a confirmed gene library, and a predicted genome using both keyword and homology based search functions. Data provided by these searches will elucidate gene family evolution in early animals. Unique research tools, including a Nematostella genetic stock library, a primer library, a literature repository and a gene expression library will provide support to the burgeoning Nematostella research community. The development of StellaBase accompanies significant upgrades to CnidBase, the Cnidarian Evolutionary Genomics Database. With the completion of the first sequenced cnidarian genome, genome comparison tools have been added to CnidBase. In addition, StellaBase provides a framework for the integration of additional species-specific databases into CnidBase. StellaBase is available at http://www.stellabase.org.

Animals↗

YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms.

We present YOGY a web-based resource for orthologous proteins from nine eukaryotic organisms: Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, Schizosaccharomyces pombe and Saccharomyces cerevisiae. Using a gene name from any of these organisms as a query, this database provides comprehensive, combined information on orthologs in other species using data from five independent resources: KOGs, Inparanoid, HomoloGene, OrthoMCL and a table of curated fission and budding yeast orthologs. Associated Gene Ontology (GO) terms of orthologs can also be retrieved for functional inference. Integrating these different and complementary datasets provides a straightforward tool to identify known and predicted orthologs of proteins from a variety of species. This resource should be useful for bench scientists looking for functional clues for their genes of interest as well as for curators looking for information that can be transferred based on orthology and for rapidly identifying the relevant GO terms as an aid to literature curation. YOGY is accessible online at http://www.sanger.ac.uk/PostGenomics/S_pombe/YOGY/.

Animals↗

TOM: a web-based integrated approach for identification of candidate disease genes.

The massive production of biological data by means of highly parallel devices like microarrays for gene expression has paved the way to new possible approaches in molecular genetics. Among them the possibility of inferring biological answers by querying large amounts of expression data. Based on this principle, we present here TOM, a web-based resource for the efficient extraction of candidate genes for hereditary diseases. The service requires the previous knowledge of at least another gene responsible for the disease and the linkage area, or else of two disease associated genetic intervals. The algorithm uses the information stored in public resources, including mapping, expression and functional databases. Given the queries, TOM will select and list one or more candidate genes. This approach allows the geneticist to bypass the costly and time consuming tracing of genetic markers through entire families and might improve the chance of identifying disease genes, particularly for rare diseases. We present here the tool and the results obtained on known benchmark and on hereditary predisposition to familial thyroid cancer. Our algorithm is available at http://www-micrel.deis.unibo.it/~tom/.

Algorithms↗

D-HaploDB: a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples.

The Definitive Haplotype Database (D-HaploDB) is a web-accessible resource of genome-wide definitive haplotypes determined from a collection of Japanese complete hydatidiform moles (CHMs), each of which carries a genome derived from a single sperm. Currently, the database contains genotypes for 281 439 common SNPs from 74 CHMs which were determined by a high-throughput array-based oligonucleotide hybridization technique. The database also presents maps of haplotype blocks and linkage disequilibrium bins together with tagSNPs that might prove useful for association studies of disease genes. Cryptic relatedness among the samples in this study is unlikely, because the formation of a CHM is a maternal event of rare sporadic occurrence, and its genotype is that of the incoming sperm. This is demonstrated by the absence of long extended shared haplotypes (ESHs). The D-HaploDB is freely accessible via the Internet at http://orca.gen.kyushu-u.ac.jp.

Chromosome Mapping↗

Collaboration among community members, local health service providers, and researchers in an urban research center in Harlem, New York.

The Urban Research Center at the Center for Urban Epidemiologic Studies brings together community members and researchers working in Harlem, New York. A Community Advisory Board (CAB) composed of community members, service providers, public health professionals, and researchers was formed to assist the Center's research and interventions and to guide community partnerships. Through a collaborative process, the CAB identified three public health problems-substance use, infectious diseases, and asthma-as action priorities. To deal with substance use, the Center created a Web-based resource guide for service providers and a "survival guide" for substance users, designed to improve access to community services. To deal with infectious diseases, the Center is collaborating with local community-based organizations on an intervention that trains injection drug users to serve as peer mentors to motivate behavior change among other injection drug users. To deal with asthma, the Center is collaborating with community child care providers on an educational intervention to increase asthma awareness among day care teaching staff, enhance communication between staff and families, and improve the self-management skills of children with asthma. The Center's experience has demonstrated that active communities and responsive researchers can establish partnerships that improve community health.

Adolescent↗

MEDICOL: online learning in medicine and dentistry.

OBJECTIVE: MEDICOL (Medicine and Dentistry Integrated Curriculum Online) provides a variety of Web-based resources that act as important adjuncts to all the teaching components of the medical and dental undergraduate curriculum. It uses WebCT, a course-management system, to provide the following educational functions: (1) track students' progress and present course information such as time-tables, learning objectives, handout materials, images, references, course assignments, and evaluations; (2) promote student-to-student and student-to-instructor interactions (through e-mail and bulletin boards); and (3) deliver self-directed learning components, including weekly self-assessment quizzes that provide immediate feedback and multimedia learning modules (clinical skills, radiology, evidence-based medicine, etc.). DESCRIPTION: The University of British Columbia Faculties of Medicine and Dentistry feature a problem-based learning (PBL) curriculum in which students access many of the same tools they will utilize in their professional practice. In the PBL curriculum, students must access the relevant clinical data and educational resources. A MEDICOL site has also been developed for medical students to use during their rural family practice, a four- to six-week experience in the summer after their second year. This site has been designed to be a supplemental learning environment for not only these students, but also for their physician preceptors. It is intended to foster communication among participants, bring new resources to the rural setting, and allow preceptors to develop their Internet skills with the help of students who are already familiar with the electronic environment. The MEDICOL sites enable the exchange of information about the learning issues between, as well as within, tutorial groups. MEDICOL also provides students with faculty-reviewed resources that are listed online; multimedia presentations; and access to histology, radiology, and pathology images through an online image database. Each week, students have access to a new interactive and automatically graded self-assessment quiz for individual study. These quizzes test learning objectives from tutorial, lecture, and lab material for each week of the curriculum and are modeled after summative examinations held twice each year. Question authors provide immediately accessible quality feedback to students. A comprehensive quiz databank of approximately 1,500 questions has been attained. WebCT enables MEDICOL to deliver anonymous, online program-evaluation questionnaires during clinical clerkships (resulting in a 99% response rate after a few e-mail reminders), with easy and timely data collection and reporting methods. Summative assessments have also been delivered through MEDICOL. DISCUSSION: Use statistics indicate that over 90% of students regularly use the MEDICOL sites and have found them helpful. University of British Columbia medical school enrollment will increase because of collaborations with campuses and medical centers across the province. MEDICOL will likely play an increased role in distance learning by continuing to deliver the resources already described, as well as facilitating synchronous communications (e.g., PBL chat rooms) and teaching (e.g., video-streamed lectures) to students located across the province.

Education, Dental↗

An initial radiation safety needs assessment of Costa Rica: the South Texas Chapter of the Health Physics Society's strategic planning appraisal for participation in the "Radiation Safety Without Borders" initiative.

In response to the Health Physics Society's recent 'radiation safety without borders" initiative, the South Texas Chapter of the Health Physics Society selected Costa Rica as its partner country of choice. To develop an understanding of the radiation safety needs of this country, the fall 2001 University of Texas Health Science Center at Houston School of Public Health Environmental Radiation and Radioactivity class was tasked with the assignment of assessing the possible radiation safety needs and concerns for this country. The assignment culminated in a class presentation to the membership of the South Texas Chapter during its annual fall meeting. Using library and web based resources, tile students reviewed a number of public health and radiation-related topics. Life expectancies were found to be equivalent to the United States, even though significant differences in per capita health expenditures were noted. Costa Rica exhibited lower population mortality rates from major causes such as cardiovascular diseases, neoplasms, and external sources. Maternal and infant mortality rates were found to be much higher in Costa Rica than in the United States. Naturally occurring radiation sources such as uranium deposits were not identified as apparent major radiation issues of concern, although ultraviolet radiation exposures are consistently high. Several recent events in the country and the region involving patient overexposures suggest that concerns are likely focused on ensuring the proper use and maintenance of healing arts radiation equipment. The lack of available information on radioactive waste disposal suggests that waste handling also may be an issue warranting attention. The exercise proved to be very educational for the students, and the information gathered will serve to focus the Chapter's efforts when technical exchanges are initiated. The importance of linking this initiative to other existing programs within the country is also discussed.

Costa Rica↗

Issues in preparedness for biologic terrorism: a perspective for critical care nursing.

Although the use of microorganisms as weapons is as old a practice as war itself, the sense of our collective vulnerability to these agents has seldom been as great. The events of late 2001 demonstrated that the United States is vulnerable to terrorist attack carried out by highly motivated, organized, funded, and trained individuals. It is our collective good fortune that the perpetrator of the anthrax mailings was not bent on destruction of the scale witnessed on September 11, 2001. Because acute care and critical care nurses are on the forefront of community disease surveillance, they must be aware of the signs and symptoms of illness that may indicate that a biological attack has taken place. Many symptoms of infection or intoxication by biological warfare agents (bacterial, viral, and toxic) are nonspecific and flulike in nature, at least early in the disease process. The essential details of the presentation, diagnosis, treatment, and prophylaxis of the biological warfare agents that merit greatest concern are provided, and five biological warfare agents of particular interest are described in detail: anthrax, ricin (castor bean) toxin, smallpox, plague, and tularemia. Recommendations are given for additional Web-based resources to allow further study.

Biological Warfare↗