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PubMedDate not supplied

The basis for using the Internet to support the information needs of primary care.

Synthesizing the state of the art from the published literature, this review assesses the basis for employing the Internet to support the information needs of primary care. The authors survey what has been published about the information needs of clinical practice, including primary care, and discuss currently available information resources potentially relevant to primary care. Potential methods of linking information needs with appropriate information resources are described in the context of previous classifications of clinical information needs. Also described is the role that existing terminology mapping systems, such as the National Library of Medicine's Unified Medical Language System, may play in representing and linking information needs to answers.

Academic Medical Centers↗
PubMed2006

A survey of the intestinal transcriptomes of the hookworms, Necator americanus and Ancylostoma caninum, using tissues isolated by laser microdissection microscopy.

The gastrointestinal tracts of multi-cellular blood-feeding parasites are targets for vaccines and drugs. Recently, recombinant vaccines that interrupt the digestion of blood in the hookworm gut have shown efficacy, so we explored the intestinal transcriptomes of the human and canine hookworms, Necator americanus and Ancylostoma caninum, respectively. We used Laser Microdissection Microscopy to dissect gut tissue from the parasites, extracted the RNA and generated cDNA libraries. A total of 480 expressed sequence tags were sequenced from each library and assembled into contigs, accounting for 268 N. americanus genes and 276 A. caninum genes. Only 17% of N. americanus and 36% of A. caninum contigs were assigned Gene Ontology classifications. Twenty-six (9.8%) N. americanus and 18 (6.5%) A. caninum contigs did not have homologues in any databases including dbEST-of these novel clones, seven N. americanus and three A. caninum contigs had Open Reading Frames with predicted secretory signal peptides. The most abundant transcripts corresponded to mRNAs encoding cholesterol-and fatty acid-binding proteins, C-type lectins, Activation-Associated Secretory Proteins, and proteases of different mechanistic classes, particularly astacin-like metallopeptidases. Expressed sequence tags corresponding to known and potential recombinant vaccines were identified and these included homologues of proteases, anti-clotting factors, defensins and integral membrane proteins involved in cell adhesion.

Amino Acid Sequence↗
PubMed2000

Evidence-based medicine training in internal medicine residency programs a national survey.

To characterize evidence-based medicine (EBM) curricula in internal medicine residency programs, a written survey was mailed to 417 program directors of U.S. internal medicine residency programs. For programs offering a freestanding (dedicated curricular time) EBM curriculum, the survey inquired about its objectives, format, curricular time, attendance, faculty development, resources, and evaluation. All directors responded to questions regarding integrating EBM teaching into established educational venues. Of 417 program directors, 269 (65%) responded. Of these 269 programs, 99 (37%) offered a freestanding EBM curriculum. Among these, the most common objectives were performing critical appraisal (78%), searching for evidence (53%), posing a focused question (44%), and applying the evidence in decision making (35%). Although 97% of the programs provided MEDLINE, only 33% provided Best Evidence or the Cochrane Library. Evaluation was performed in 37% of the freestanding curricula. Considering all respondents, most programs reported efforts to integrate EBM teaching into established venues, including attending rounds (84%), resident report (82%), continuity clinic (76%), bedside rounds (68%), and emergency department (35%). However, only 51% to 64% of the programs provided on-site electronic information and 31% to 45% provided site-specific faculty development. One third of the training programs reported offering freestanding EBM curricula, which commonly targeted important EBM skills, utilized the residents' experiences, and employed an interactive format. Less than one half of the curricula, however, included curriculum evaluation, and many failed to provide important medical information sources. Most programs reported efforts to integrate EBM teaching, but many of these attempts lacked important structural elements.

Curriculum↗
PubMed2000

A sea urchin genome project: sequence scan, virtual map, and additional resources.

Results of a first-stage Sea Urchin Genome Project are summarized here. The species chosen was Strongylocentrotus purpuratus, a research model of major importance in developmental and molecular biology. A virtual map of the genome was constructed by sequencing the ends of 76,020 bacterial artificial chromosome (BAC) recombinants (average length, 125 kb). The BAC-end sequence tag connectors (STCs) occur an average of 10 kb apart, and, together with restriction digest patterns recorded for the same BAC clones, they provide immediate access to contigs of several hundred kilobases surrounding any gene of interest. The STCs survey >5% of the genome and provide the estimate that this genome contains approximately 27,350 protein-coding genes. The frequency distribution and canonical sequences of all middle and highly repetitive sequence families in the genome were obtained from the STCs as well. The 500-kb Hox gene complex of this species is being sequenced in its entirety. In addition, arrayed cDNA libraries of >10(5) clones each were constructed from every major stage of embryogenesis, several individual cell types, and adult tissues and are available to the community. The accumulated STC data and an expanding expressed sequence tag database (at present including >12, 000 sequences) have been reported to GenBank and are accessible on public web sites.

Aging↗
PubMed1995

A novel DNA-binding domain that may form a single zinc finger motif.

MNB1a is a DNA-binding protein from maize that interacts with the 35S promoter of cauliflower mosaic virus. This protein did not show significant homologies with any other DNA-binding protein and MNB1a seemed to be a member of a multigene family. In this study, isolation of cDNAs from the gene family to which MNB1a belongs revealed a unique conserved domain, referred to herein as the Dof domain, that contains a novel cysteine-rich motif for a single putative zinc finger. The amino acid sequence of the Dof domain and the arrangement of cysteine residues in this domain differ from those of known zinc finger motifs. However, the Dof domain was shown to be a DNA-binding domain that required Zn2+ ions for activity. Mutations at cysteine residues eliminated the DNA-binding activity of MNB1a. Thus, the Dof domain may be classified as a novel zinc finger motif. In addition, Southern blot analysis and a survey of DNA databases suggested that proteins that include Dof domains might exist in other eukaryotes, at least in the plant kingdom.

Amino Acid Sequence↗
PubMed2001

YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information.

The BioKnowledge Library is a relational database and web site (http://www.proteome.com) composed of protein-specific information collected from the scientific literature. Each Protein Report on the web site summarizes and displays published information about a single protein, including its biochemical function, role in the cell and in the whole organism, localization, mutant phenotype and genetic interactions, regulation, domains and motifs, interactions with other proteins and other relevant data. This report describes four species-specific volumes of the BioKnowledge Library, concerned with the model organisms Saccharomyces cerevisiae (YPD), Schizosaccharomyces pombe (PombePD) and Caenorhabditis elegans (WormPD), and with the fungal pathogen Candida albicans (CalPD). Protein Reports of each species are unified in format, easily searchable and extensively cross-referenced between species. The relevance of these comprehensively curated resources to analysis of proteins in other species is discussed, and is illustrated by a survey of model organism proteins that have similarity to human proteins involved in disease.

Animals↗
PubMed1994

Computer skills and attitudes to computer-aided learning among medical students.

One hundred and forty-four third-year medical students at the University of Edinburgh were surveyed as to levels of computing skills and confidence in carrying out computing tasks. Attitudes to computer-aided learning for clinical teaching were also measured. Thirty-one per cent of students had not used a computer in the previous year and 38% had not used a computer outside supervised laboratory work. Twenty-two per cent had never used the university library computerized catalogue and 43% had never carried out a medline search using the library CD-ROM. Students were not confident of their ability to carry out simple computing tasks. Fifty-four per cent said they would need support or instruction in printing out a document, 69% were not confident they could copy a file onto a disk and 74% did not believe they could independently create a graph in a document. Students who had completed an intercalated honours year were significantly more skilled and confident in computing tasks. Attitudes to computer-aided learning were related to computing confidence. Medical students who have not acquired basic computer information technology (IT) skills by the third year of undergraduate training are unlikely to do so in the final hospital-based years. Undergraduate curricula for medical students must incorporate specific computer (IT) training.

Attitude to Computers↗
PubMed2004

RACE and RAGE cloning in parasitic microbial eukaryotes.

Many gene-cloning strategies and gene survey often provide partial sequence data. To exploit the information from these partial sequences numerous PCR-based approaches have been developed to clone full-length open reading frames. These approaches can be successful using small quantities of cDNA or genomic DNA as starting material and avoid the need to go through the complex and tedious process of constructing and screening gene libraries. Here we present two of these approaches, called RACE and RAGE, we used to successfully clone partial and full-length ORFs from amitochondriate parasitic microbial eukaryotes. The RACE approach uses cDNA as template for PCR cloning whereas RAGE uses genomic DNA. These two approaches were used to complement each other to provide full-length genes. The amitochondriate microbial eukaryotes we are investigating are of interest from both evolutionary and biomedical perspectives. We have investigated genes of mitochondrial origins in the obligate intracellular parasite called microsporidia. In these organisms spores are the only source of material that can be isolated from host cells and typically yield small amount of mRNA and genomic DNA for cloning. A full-length mitochondrial Hsp70 could be cloned and sequenced and specific antibody raised against a fusion protein. The highly specific antibody allowed us to demonstrate for the first time the presence of mitochondrial-like organelles in microsporidia.

Animals↗
PubMed1999

Large-scale gene expression data analysis: a new challenge to computational biologists.

The use of high-density DNA arrays to monitor gene expression at a genome-wide scale constitutes a fundamental advance in biology. In particular, the expression pattern of all genes in Saccharomyces cerevisiae can be interrogated using microarray analysis where cDNAs are hybridized to an array of each of the approximately 6000 genes in the yeast genome. In this survey I review three recent experiments related to transcriptional regulation and discuss the great challenge for computational biologists trying to extract functional information from such large-scale gene expression data.

Animals↗
PubMed1988

Chromatographic resolution and immunologic identification of the alpha 40 and alpha 41 subunits of guanine nucleotide-binding regulatory proteins from bovine brain.

A guanine nucleotide-binding regulatory protein (G protein), with subunits designated as alpha 40 beta gamma, was identified and partially resolved from two other purified G proteins, Go (alpha 39 beta gamma) and Gi (alpha 41 beta gamma), found in bovine brain. The alpha 40 G protein subunit served as a substrate for ADP-ribosylation catalyzed by Bordetella pertussis toxin, as did alpha 39 and alpha 41. alpha 40 was shown to be closely related to, but distinct from, alpha 41 by reaction with various peptide antisera. An antiserum generated against a peptide derived from the sequence of a Gi alpha clone isolated from a rat C6 glioma cDNA library (Itoh, H., Kozasa, T., Nagata, S., Nakamura, S., Katada, T., Ui, M., Iwai, S., Ohtsuka, E., Kawasaki, H., Suzuki, K., and Kaziro, Y. (1986) Proc. Natl. Acad. Sci. U. S. A. 83, 3776-3780) reacted with alpha 40 to the exclusion of all other alpha subunits tested. Another antiserum generated against a peptide derived from an analogous region of a different Gi alpha clone from a bovine brain cDNA library (Nukuda, T., Tanabe, T., Takahashi, H., Noda, M., Haga, K., Haga, T., Ichiyama, A., Kangawa, K., Hiranaga, M., Matsuo, H., and Numa, S. (1986) FEBS Lett. 197, 305-310) reacted exclusively with alpha 41. Evidence is given for the existence of another form of alpha 41 that did not react with either of these two peptide antisera. The antisera were used to survey various rat tissues for the expression of alpha 40 and alpha 41.

Adenosine Diphosphate Ribose↗
PubMed1992

Strictosidine synthase from Rauvolfia serpentina: analysis of a gene involved in indole alkaloid biosynthesis.

The gene for strictosidine synthase (str1), the enzyme which catalyzes the stereospecific condensation of tryptamine and secologanin to form the key indole alkaloid 3 alpha(S)-strictosidine has been isolated from genomic libraries prepared from Rauvolfia serpentina (India) and from Rauvolfia mannii (West Africa). The gene, str1, contained no introns and showed 100% nucleotide sequence homology over 1180 bp, encompassing the entire reading frame, between the two species. Transcription of the R. serpentina gene was found to start 81 nucleotides upstream from the AUG (26 nucleotides downstream from the TATA box). Transient expression assays in Nicotiana plumbaginifolia protoplasts of the R. serpentina str1 5'-noncoding region fused to the beta-glucuronidase reporter gene revealed promoter activity equivalent to 4 +/- 2% of that of 35 S CaMV promoter control. A series of truncated segments of the str1 promoter region indicated the presence of three areas of slight, but reproducible, negative control. Gel retardation assays demonstrated that several regions of the 5'-flanking sequences specifically bound nuclear protein from R. serpentina and that at least one region does not bind R. mannii nuclear protein. A survey of the expression of str1 in the R. serpentina plant suggested that strictosidine synthase poly(A)+ RNA was present predominantly, but not exclusively, in the root. This result correlated well with the distribution of both enzyme activity and indole alkaloids which were also predominant in the root, but, in general, distributed throughout the shrub.

Amino Acid Sequence↗
PubMed2005

An expressed sequence tag survey of gene expression in the pond snail Lymnaea stagnalis, an intermediate vector of trematodes [corrected].

The pond snail Lymnaea stagnalis is an intermediate vector for the liver fluke Fasciola hepatica, a common parasite of ruminants and humans. Yet, despite being a disease of medical and economic importance, as well as a potentially useful comparative tool, the genetics of the relationship between Lymnaea and Fasciola has barely been investigated. As a complement to forthcoming F. hepatica expressed sequence tags (ESTs), we generated 1320 ESTs from L. stagnalis central nervous system (CNS) libraries. We estimate that these sequences derive from 771 different genes, of which 374 showed significant similarity to proteins in public databases, and 169 were similar to ESTs from the snail vector Biomphalaria glabrata. These L. stagnalis ESTs will provide insight into the function of the snail CNS, as well as the molecular components of behaviour and response to parasitism. In the future, the comparative analysis of Lymnaea/Fasciola with Biomphalaria/Schistosoma will help to understand both conserved and divergent aspects of the host-parasite relationship. The L. stagnalis ESTs will also assist gene prediction in the forthcoming B. glabrata genome sequence. The dataset is available for searching on the world-wide web at http://zeldia.cap.ed.ac.uk/mollusca.html.

Amino Acid Sequence↗
PubMed2004

Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats.

Sugarcane microsatellites or simple sequence repeats (SSR) were developed in an economical and practical way by mining EST databases. A survey in the SUCEST (sugarcane EST) database revealed a total of 2005 clusters out of 43,141 containing SSRs. Of these, 8.2% were dinucleotide, 30.5% were trinucleotide, and 61.3% were tetranucleotide repeats. Except for dinucleotides, the CG-rich motif types were the most common. Differences in abundance of trinucleotide motif types were observed between EST-SSRs and those isolated from sugarcane genomic libraries. Among the different cDNA libraries used for EST sequencing, SSRs were more frequent in the ones derived from leaf roll (LR). Twenty-three out of 30 tested SSRs produced scorable polymorphisms in 18 sugarcane commercial clones. These EST-SSRs showed a moderate level of polymorphism with some SSRs producing unique fingerprints. The number of alleles observed among the 18 clones evaluated varied from 2 to 15, with an average of 6.04 alleles/locus. The polymorphism information content (PIC) values ranged from 0.28 to 0.90 with a mean of 0.66. The EST-SSRs screened over both parents (SP 80-180; SP 80-4966) and 6 F1 individuals produced 52 segregating markers that could potentially be used for sugarcane mapping. The EST-SSRs were found in clusters that had significant homology to proteins involved in important metabolic pathways such as sugar biosynthesis, proving that EST-SSRs are a valuable tool for the construction of a functional sugarcane map.

Alleles↗
PubMed1986

How computers are used in pathology education.

How are computers being used to teach pathology? Of 129 major medical teaching institutions surveyed, 63 institutions responded and 37 were using computers in pathology education. Applications include examination, instruction and consultation, case simulation, and course evaluation.

Computer-Assisted Instruction↗
PubMed2005

Use of Internet audience measurement data to gauge market share for online health information services.

BACKGROUND: The transition to a largely Internet and Web-based environment for dissemination of health information has changed the health information landscape and the framework for evaluation of such activities. A multidimensional evaluative approach is needed. OBJECTIVE: This paper discusses one important dimension of Web evaluation-usage data. In particular, we discuss the collection and analysis of external data on website usage in order to develop a better understanding of the health information (and related US government information) market space, and to estimate the market share or relative levels of usage for National Library of Medicine (NLM) and National Institutes of Health (NIH) websites compared to other health information providers. METHODS: The primary method presented is Internet audience measurement based on Web usage by external panels of users and assembled by private vendors-in this case, comScore. A secondary method discussed is Web usage based on Web log software data. The principle metrics for both methods are unique visitors and total pages downloaded per month. RESULTS: NLM websites (primarily MedlinePlus and PubMed) account for 55% to 80% of total NIH website usage depending on the metric used. In turn, NIH.gov top-level domain usage (inclusive of NLM) ranks second only behind WebMD in the US domestic home health information market and ranks first on a global basis. NIH.gov consistently ranks among the top three or four US government top-level domains based on global Web usage. On a site-specific basis, the top health information websites in terms of global usage appear to be WebMD, MSN Health, PubMed, Yahoo! Health, AOL Health, and MedlinePlus. Based on MedlinePlus Web log data and external Internet audience measurement data, the three most heavily used cancer-centric websites appear to be www.cancer.gov (National Cancer Institute), www.cancer.org (American Cancer Society), and www.breastcancer.org (non-profit organization). CONCLUSIONS: Internet audience measurement has proven useful to NLM, with significant advantages compared to sole reliance on usage data from Web log software. Internet audience data has helped NLM better understand the relative usage of NLM and NIH websites in the intersection of the health information and US government information market sectors, which is the primary market intersector for NLM and NIH. However important, Web usage is only one dimension of a complete Web evaluation framework, and other primary research methods, such as online user surveys, usability tests, and focus groups, are also important for comprehensive evaluation that includes qualitative elements, such as user satisfaction and user friendliness, as well as quantitative indicators of website usage.

Humans↗
PubMed2006

Biogeography and landscape-scale diversity of the dominant Crenarchaeota of soil.

We surveyed the diversity of soil Archaea across a large scale elevational gradient of ecosystem types, from foothills forest to alpine tundra in the Front Range of the Rocky Mountains. We used a dilution technique to sequence the single most abundant archaeal 16S rDNA sequence in each of the 40 soil cores distributed across the gradient to compare our results to those of typical 16S clone library studies. We found a greater diversity of sequences than has typically been found in clone library studies from a single site or core, identifying sequences both from the Terrestrial Group and the FFSB Group at several sites. We did not observe any significant environmental correlates with the dominant sequence type, nor was there any relationship between the spatial distance between samples and the phylogenetic similarity of the dominant sequence types. Despite using a very different methodology, our collective results are in remarkably good agreement with other studies of soil Crenarchaeota in terms of the diversity and relative abundance of sequence types identified. We are able to identify two instances of very tightly clustered sequences which we suggest are the results of global selective sweeps-one closely related to SCA1145, an abundant globally distributed group within the Terrestrial Group of Crenarchaeota, and another nested within the more basal FFSB group of sequences. We replicated our sequence results at two levels: first, by repeating the dilution and PCR processes from the same soil core DNA extraction, and second, by performing a replicate DNA extraction from the same homogenized soil core sample. Pairs of sequences produced by the dilution replicates were significantly more similar than the pairs of sequences produced by the extraction replicates, suggesting that soil Crenarchaeota exists in highly localized and discrete clonal populations.

Base Sequence↗
PubMed2005

Delivering the English smoking treatment services.

BACKGROUND: This paper describes how smoking treatment services in England were delivered beyond the initial set-up phase and explores key factors affecting their development. Services were expected to treat smokers in line with the evidence-base and were issued with government guidance regarding the type of interventions that should be offered. One factor complicating this was the issue of service funding. Funding was initially issued for a 3-year period and although this was extended on two occasions, these extensions were both announced close to the end of funding periods. OBJECTIVES: To critically assess key elements in the delivery of the English cessation services, including the nature of treatments offered and the impact of short-term funding on staffing. METHODS: A national postal survey of smoking cessation coordinators in April 2002. Semi-structured interviews with 50 smoking cessation staff in two health regions in autumn 2001, followed by further interviews with 28 staff in the same areas in the autumn of 2002. RESULTS: Treatment was delivered in a wide range of venues, ranging from primary care to local authority-owned premises such as town halls and libraries. Most services offered both one-to-one and group support, although interviewees reported an increase in demand for one-to-one support from clients. Pharmacotherapies were used widely; by 2002, 99% of coordinators reported that their advisers recommended nicotine replacement therapy (NRT) to clients, and 95% bupropion. However, prior to April 2001 bupropion was available on prescription, but NRT was not and this variable access to pharmacotherapies posed problems for services. Coordinators reported that the short-term nature of funding made recruiting and retaining staff difficult and interviews revealed that they believed a longer period of protected funding was required for services to demonstrate their effectiveness. CONCLUSIONS: As English smoking treatment services developed, lessons were learned that could inform the development of services in other health systems. First, early guidance from government can encourage services to adhere to evidence-based treatment. Secondly, treatment needs to be accessible to smokers and thus there must be a flexible approach to implementation at local level. Thirdly, the availability of nicotine addiction and behavioural therapies should be coordinated to minimize barriers and maximize uptake. Finally, fixed-term funding can exacerbate staff recruitment and retention difficulties and countries establishing treatment services need to consider carefully the initial funding period that is required for stable services to become established within their health systems.

Costs and Cost Analysis↗
PubMed1997

Extensive random mutagenesis analysis of the Na+/K+-ATPase alpha subunit identifies known and previously unidentified amino acid residues that alter ouabain sensitivity--implications for ouabain binding.

Random mutagenesis with ouabain selection has been used to comprehensively scan the extracellular and transmembrane domains of the alpha1 subunit of the sheep Na+/K+-ATPase for amino acid residues that alter ouabain sensitivity. The four random mutant libraries used in this study include all of the transmembrane and extracellular regions of the molecule as well as 75% of the cytoplasmic domains. Through an extensive number of HeLa cell transfections of these libraries and subsequent ouabain selection, 24 ouabain-resistant clones have been identified. All previously described amino acids that confer ouabain resistance were identified, confirming the completeness of this random mutagenesis screen. The amino acid substitutions that confer the greatest ouabain resistance, such as Gln111-->Arg, Asp121-->Gly, Asp121-->Glu, Asn122-->Asp, and Thr797-->Ala were identified more than once in this study. This extensive survey of the extracellular and transmembrane regions of the Na+/K+-ATPase molecule has identified two new regions of the molecule that affect ouabain sensitivity: the H4 and the H10 transmembrane regions. The new substitutions identified in this study are Leu330-->Gln, Ala331-->Gly, Thr338-->Ala, and Thr338-->Asn in the H4 transmembrane domain and Phe982-->Ser in the H10 transmembrane domain. These substitutions confer modest increases in the concentration of cardiac glycoside needed to produce 50% inhibition of activity (IC50 values), 3.1-7.9-fold difference. The results of this extensive screening of the Na+/K+-ATPase alpha1 subunit to identify amino acids residues that are important in ouabain sensitivity further supports our hypothesis that the H1-H2 and H4-H8 regions represent the major binding sites for the cardiac glycoside class of drugs.

Amino Acid Sequence↗