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PubMed2002

South Cheshire Local Multi-disciplinary Evidence Centre: an evaluation.

The South Cheshire Local Multidisciplinary Evidence Centre (LMEC) was a two-year project commenced in March 1998 and completed in April 2000. The project aimed to develop an information service to enable all primary and community care staff in South Cheshire to access high-quality evidence and thus to improve patient care. The LMEC gave access from the workplace to both physical and electronic resources to support clinical governance and lifelong learning, with a strong emphasis on evidence-based material. Automation of the library catalogue enabled its inclusion on the website. The project developed enquiry and document delivery services and provided training on using the LMEC and on critical appraisal. An evaluation carried out at the end of the project showed that over 120 primary and community care staff had used the LMEC and were positive about the service. As Clinical Governance, the NHSnet, and plans for continuing professional development are implemented, the LMEC is one model for a Local Health Information Service outlined in the NHS IT strategy.

Education, Medical, Continuing↗
PubMed2006

Experimental approaches to identify non-coding RNAs.

Cellular RNAs that do not function as messenger RNAs (mRNAs), transfer RNAs (tRNAs) or ribosomal RNAs (rRNAs) comprise a diverse class of molecules that are commonly referred to as non-protein-coding RNAs (ncRNAs). These molecules have been known for quite a while, but their importance was not fully appreciated until recent genome-wide searches discovered thousands of these molecules and their genes in a variety of model organisms. Some of these screens were based on biocomputational prediction of ncRNA candidates within entire genomes of model organisms. Alternatively, direct biochemical isolation of expressed ncRNAs from cells, tissues or entire organisms has been shown to be a powerful approach to identify ncRNAs both at the level of individual molecules and at a global scale. In this review, we will survey several such wet-lab strategies, i.e. direct sequencing of ncRNAs, shotgun cloning of small-sized ncRNAs (cDNA libraries), microarray analysis and genomic SELEX to identify novel ncRNAs, and discuss the advantages and limits of these approaches.

Gene Expression Profiling↗
PubMed2006

Cracking the egg: molecular dynamics and evolutionary aspects of the transition from the fully grown oocyte to embryo.

Fully grown oocytes (FGOs) contain all the necessary transcripts to activate molecular pathways underlying the oocyte-to-embryo transition (OET). To elucidate this critical period of development, an extensive survey of the FGO transcriptome was performed by analyzing 19,000 expressed sequence tags of the Mus musculus FGO cDNA library. Expression of 5400 genes and transposable elements is reported. For a majority of genes expressed in mouse FGOs, homologs transcribed in eggs of Xenopus laevis or Ciona intestinalis were found, pinpointing evolutionary conservation of most regulatory cascades underlying the OET in chordates. A large proportion of identified genes belongs to several gene families with oocyte-restricted expression, a likely result of lineage-specific genomic duplications. Gene loss by mutation and expression in female germline of retrotransposed genes specific to M. musculus is documented. These findings indicate rapid diversification of genes involved in female reproduction. Comparison of the FGO and two-cell embryo transcriptomes demarcated the processes important for oogenesis from those involved in OET and identified novel motifs in maternal mRNAs associated with transcript stability. Discovery of oocyte-specific eukaryotic translation initiation factor 4E distinguishes a novel system of translational regulation. These results implicate conserved pathways underlying transition from oogenesis to initiation of development and illustrate how genes acquire and lose reproductive functions during evolution, a potential mechanism for reproductive isolation.

Amino Acid Sequence↗
PubMed2006

A journal club is an effective tool for assisting librarians in the practice of evidence-based librarianship: a case study.

OBJECTIVE: To establish a journal club for librarians, which aimed to develop appraisal skills and assist in the application of research to practice. METHODS: Fourteen health librarians were invited to attend a journal club. Each month a librarian was responsible for preparing a scenario, choosing a research paper, and selecting a checklist. The paper was appraised by the club, and a critically appraised topic (CAT) prepared. Six months later, a questionnaire was sent to all librarians. RESULTS: Six out of 14 librarians attended the journal club and five out of six returned the questionnaire. All five agreed that attending the journal club helped them develop appraisal skills, write a CAT and be more critical of research. Four agreed they always identified a research paper first, then formulated a question. One librarian agreed that applying results to their own practice was difficult, one disagreed and three were neutral. CONCLUSION: Journal clubs can be effective at developing appraisal skills and writing a CAT, as well as increasing the reading of library research. Librarians still need assistance in identifying and using questions directly from their own practice. The journal club has helped some librarians to apply evidence to practice, but others find the research is not always directly relevant.

Competency-Based Education↗
PubMed2006

Evaluation of a hospital medical library class for NICU nurses.

A library class was designed and offered to new nurses from the Neonatal Intensive Care Unit at the Children's Hospital of Michigan between 2003 and 2005. The class was intended to increase their knowledge of quality health information resources and to assist them with their smooth transition to a new health care organization. The goal of the library training class was to develop the nurses' awareness and knowledge of the library services and online resources on the organization Intranet and to improve their skills in finding reliable information related to patient care, patient parent education, and research. An evaluation study was conducted to assess the effectiveness of the library class. Although the findings demonstrated strengths of the library class, they also revealed some areas for improvement. The data gathered resulted in a number of recommendations regarding library instruction design and evaluation.

Female↗
PubMed2002

Norwegian Twin Registers and Norwegian twin studies--an overview.

The Norwegian Twin Registers include several sets of population-based sub-registers, and covers twin pairs born between 1895 and today. Except for the missing birth years 1960 to 1967, the register is almost complete. Most of the register contains information about both same-sexed and opposite-sexed twin pairs, except for twin pairs born between 1946 and 1960, where only same-sexed twins are registered. In a substantial part of the register, information about zygosity is obtained, mainly by a mailed questionnaire and in some cases supported by DNA testing. These are the birth years 1915 to 1960 and the birth years 1967 to 1979. Zygosity information is further obtained in the different twin studies derived from the twin register. In 1990 the whole register was made available in a computerized form. Several twin studies have been derived from the different parts of the register. In this article, studies from the two earliest parts of the register are reviewed and grouped by recruitment specifics. Finally, future plans for the register and twin studies are discussed.

Alzheimer Disease↗
PubMedDate not supplied

Community resources and determinants of the future health of Manitobans.

BACKGROUND: Life history studies in health show that some of the key determinants of health inequalities lie in biological and social experiences at the earliest times of life. The objectives of this research were to describe the regional distribution of childhood determinants of adult health, such as school achievement, and the environments which contribute to their development. METHODS: Using Manitoba data from the National Population Health Survey, the National Longitudinal Survey on Children and Youth, the Department of Education, Training and Youth, the Department of Family Services and Housing, the Library Association website and the Agriculture and Food website, the regional distribution of Grade 3 standards test scores and neighbourhood resources such as child care services, libraries, sports participation and food costs were determined for 12 Regional Health Authorities and 12 Winnipeg Community Areas, ranked by a measure of population healthiness, the premature mortality rate. Findings were also reported by income level and larger geographic regions. RESULTS: Children living in neighbourhoods with less healthy populations were more likely to have poorer school performance, as indicated by Grade 3 math standards test scores. They were-also more likely to change schools, less likely to participate in sports, and had decreased access to affordable food and licenced day care. They had similar access to library books as children living in more healthy neighbourhoods, although book lending rates were not measured. CONCLUSION: We documented regional variation in the availability of resources to support healthy childhood development.

Child↗
PubMed2005

Understanding nurses' information needs and searching behaviour in acute care settings.

UNLABELLED: We report the results of a pilot study designed to describe nurses' information needs and searching behaviour in acute care settings. Several studies have indicated that nurses have unmet information needs while delivering care to patients. AIM: Identify the information needs of nurses in acute care settings. METHODS: Nurses at three hospitals were asked to use an information retrieval tool (CPG Viewer). A detailed log of their interactions with the tool was generated. RESULTS AND CONCLUSIONS: Our findings suggest that nurses' information needs are different from what is reported in the literature in terms of physicians' information needs. Questions regarding a nursing procedure or protocol were the most common needs nurses had.

Attitude of Health Personnel↗
PubMed1985

Demonstration of transthyretin mRNA in the brain and other extrahepatic tissues in the rat.

Studies were conducted to ascertain if transthyretin mRNA was present in extrahepatic tissues of the rat. A trnasthyretin cDNA clone was isolated from a lambda gt11 human liver cDNA library by antibody screening and its identity was confirmed by nucleotide sequence analysis. This transthyretin cDNA clone was used to survey poly(A+) RNA isolated from 12 different rat tissues for transthyretin mRNA by Northern blot analysis. The liver contained the highest level of transthyretin mRNA and this level was not altered by the vitamin A status of the rat. A significant amount of transthyretin mRNA was found in the brain (30% of the level of the liver) which was localized in specific regions of the brain. In addition, detectable levels of transthyretin mRNA (1% to 2% of that of the liver) were observed in the stomach, heart, skeletal muscle, and spleen. Translation of brain poly(A+) RNA in rabbit reticulocyte lysates and immunoprecipitation of the translation products with anti-transthyretin antiserum resulted in a protein band of the same size as liver pre-transthyretin. Liver pre-transthyretin was processed by the cotranslational addition of dog pancreas microsomal membranes to a protein that migrated coincidentally with monomeric serum transthyretin. These data suggest that transthyretin in the brain and the cerebrospinal fluid results from de novo synthesis and that transthyretin may play a significant physiological function, as yet unknown, within the nervous system.

Animals↗
PubMed2025

Enzymatic depletion of transposable elements in sequencing libraries and its application for genotyping multiplexed CRISPR-edited plants.

Whole-genome sequencing has become a common strategy to genotype individual plants of interest. Although a limited number of genomic regions usually need to be surveyed with this strategy, excess sequencing information is almost always generated at an appreciable financial cost. Repetitive sequences (e.g., transposons), which can account for more than 80% of the genome of some plants, are often not required in these genotyping projects. Therefore, strategies that enrich DNA coding for the protein-coding genes prior to sequencing can lower the cost to obtain sufficient sequence information. Here, we present the development and application of methylation-sensitive reduced representation sequencing (MsRR-Seq), which relies on the cytosine methylation-sensitive restriction enzyme MspJI to deplete constitutive heterochromatic DNA before library construction. By applying MsRR-Seq to citrus and maize, we show that protein-coding genes can be enriched in sequencing datasets. We then describe the application of MsRR-Seq to facilitate the identification of complex mutants from populations of citrus plants resulting from multiplex CRISPR/Cas9 editing of four genes. Overall, this work demonstrates an easy and low-cost method to enrich non-repetitive DNA in high-throughput sequencing libraries, an approach that is especially useful for large plant genomes with an excessively high proportion of methylated repetitive sequences.

DNA Transposable Elements↗
PubMed1971

Planning and designing hospital health science libraries.

The people who plan and design hospital libraries must be aware of the environment in which the library functions. The hospital health science library operates under a different set of values and priorities from an academic library. Three methodologic studies are reported to determine hospital health science functions with comments on the significance of the data for designing: (i) the extent and possible use of books and journal collections makes it evident a hospital must act as an access point to the scholarly record; (ii) a survey of 41 hospitals shows a wide variety and combination of 33 user services; obviously what services are to be given should be decided before design; (iii) observing how different areas are used by a library's clientele shows that groups use the library differently and within certain time patterns; the arrangement of the functional areas can be better designed if quantitative data on the use of space are available.

Architecture↗
PubMed1995

Use of information sources by family physicians: a literature survey.

Analysis of the use of information sources by family physicians is important for both practical and theoretical reasons. First, analysis of the ways in which family physicians handle information may point to opportunities for improvement. Second, such efforts may lead to improvements in the methodology of literature research in general. This article reports on a survey of the literature on information use by family physicians. Eleven relevant research publications could be found. The data showed that family physicians used colleagues most often as information sources, followed by journals and books. This outcome corresponded with results in other professions. Several factors influenced the use of information sources by family physicians, including the physical, functional, and intellectual accessibility of the source; the physician's age; participation by the physician in research or education; the social context of the physician; practice characteristics; and the stage of the information-gathering process. The publications studied suggested ways to improve information gathering in the areas of computerization, education, library organization, and journal articles.

Education↗
PubMed2006

Sample size calculations for disease freedom and prevalence estimation surveys.

We developed a Bayesian approach to sample size calculations for studies designed to estimate disease prevalence that uses a hierarchical model for estimating the proportion of infected clusters (cluster-level prevalence) within a country or region. The clusters may, for instance, be villages within a region, cities within a state, or herds within a country. Our model allows for clusters with zero prevalence and for variability in prevalences among infected clusters. Moreover, uncertainty about diagnostic test accuracy and within-cluster prevalences is accounted for in the model. A predictive approach is used to address the issue of sample size selection in human and animal health surveys. We present sample size calculations for surveys designed to substantiate freedom of a region from an infectious agent (disease freedom surveys) and for surveys designed to estimate cluster-level prevalence of an endemic disease (prevalence estimation surveys). In disease freedom surveys, for instance, assuming the cluster-level prevalence for a particular infectious agent in the region is greater than a maximum acceptable threshold, a sample size combination consisting of the number of clusters sampled and number of subjects sampled per cluster can be determined for which authorities conducting the survey detect this excessive cluster-level prevalence with high predictive probability. The method is straightforward to implement using the Splus/R library emBedBUGS together with WinBUGS.

Animals↗
PubMed2005

Gene discovery and expression profile analysis through sequencing of expressed sequence tags from different developmental stages of the chytridiomycete Blastocladiella emersonii.

Blastocladiella emersonii is an aquatic fungus of the chytridiomycete class which diverged early from the fungal lineage and is notable for the morphogenetic processes which occur during its life cycle. Its particular taxonomic position makes this fungus an interesting system to be considered when investigating phylogenetic relationships and studying the biology of lower fungi. To contribute to the understanding of the complexity of the B. emersonii genome, we present here a survey of expressed sequence tags (ESTs) from various stages of the fungal development. Nearly 20,000 cDNA clones from 10 different libraries were partially sequenced from their 5' end, yielding 16,984 high-quality ESTs. These ESTs were assembled into 4,873 putative transcripts, of which 48% presented no matches with existing sequences in public databases. As a result of Gene Ontology (GO) project annotation, 1,680 ESTs (35%) were classified into biological processes of the GO structure, with transcription and RNA processing, protein biosynthesis, and transport as prevalent processes. We also report full-length sequences, useful for construction of molecular phylogenies, and several ESTs that showed high similarity with known proteins, some of which were not previously described in fungi. Furthermore, we analyzed the expression profile (digital Northern analysis) of each transcript throughout the life cycle of the fungus using Bayesian statistics. The in silico approach was validated by Northern blot analysis with good agreement between the two methodologies.

Amino Acid Sequence↗
PubMed2003

The tyranny of adenosine recognition among RNA aptamers to coenzyme A.

BACKGROUND: Understanding the diversity of interactions between RNA aptamers and nucleotide cofactors promises both to facilitate the design of new RNA enzymes that utilize these cofactors and to constrain models of RNA World evolution. In previous work, we isolated six pools of high affinity RNA aptamers to coenzyme A (CoA), the principle cofactor in biological acyltransfer reactions. Interpretation of the evolutionary significance of those results was made difficult by the fact that the affinity resin attachment strongly influenced the outcome of those selections. Here we describe the selection of four new pools isolated on a disulfide-linked CoA affinity matrix to minimize context-dependent recognition imposed by the attachment to the solid support. RESULTS: The four new aptamer libraries show no sequence or structural relation to a previously dominant CoA-binding species, even though they were isolated from the same initial random libraries. Recognition appears to be limited to the adenosine portion of the CoA--in particular the Höogsteen edge--for most isolates surveyed, even when a counter selection was employed to remove such RNAs. Two of the recovered isolates are eluted with intact CoA more efficiently than with AMP alone suggesting a possible pantotheine interaction. However, a detailed examination of recognition specificity revealed that the 3' phosphate of CoA, and not the pantotheine arm, determined recognition by these two isolates. CONCLUSION: Most aptamers that have been targeted towards cofactors containing adenosine recognize only the adenosine portion of the cofactor. They do not distinguish substituents on the 5' carbon, even when those substituents have offered hydrogen bonding opportunities and the selection conditions discouraged adenosine recognition. Beyond hydrogen bonding, additional factors that guide the selection towards adenosine recognition include aromatic stacking interactions and relatively few rotational degrees of freedom. In the present work, a sterically accessible, disulfide-linked CoA affinity resin afforded the selection of a more diverse aptamer collection then previous work with a N6 linked CoA resin.

Adenosine↗
PubMed2005

Identification of novel mediators of NF-kappaB through genome-wide survey of monocyte adherence-induced genes.

The transcription factor nuclear factor (NF)-kappaB controls the expression of genes involved in inflammation, cell proliferation, apoptosis, and differentiation. Impaired regulation of NF-kappaB has been associated with many diseases; thus, there is significant interest in therapeutic approaches based on modulation of this transcription factor. NF-kappaB activity is controlled by numerous signaling molecules, many of which are potentially to be identified. Monocytes are principal effectors of the immune system, and monocyte adherence is the first step leading to their activation and differentiation. Adherence induces activation of NF-kappaB, resulting in the induction of proinflammatory genes as well as anti-inflammatory genes, which counterbalance and limit the intensity and duration of NF-kappaB activation. Here, to identify novel mediators of NF-kappaB signaling, we used the model of monocyte adherence to perform a systematic, genome-wide survey of adherence-induced genes. Having isolated mRNAs from nonadherent and adherent primary human monocytes, we constructed suppressive subtraction hybridization libraries containing cDNAs, which were differentially regulated by adherence. Of 366 identified differentially expressed genes, most were found to be up-regulated by adherence. Having analyzed a subset of these genes, we found that the library was enriched with inhibitors of NF-kappaB. Three of those (an orphan nuclear receptor NUR77, a guanosine 5'-diphosphate/guanosine 5'-triphosphate exchange factor RABEX5, and a PRK1-associated protein AWP1) were particularly potent inhibitors of NF-kappaB activation. Thus, the collection of monocyte adherence-regulated genes represents a rich source for the identification of novel components of the machinery that controls NF-kappaB activation.

Adaptor Proteins, Signal Transducing↗