Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Library Collection Development”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,135 records · Page 63Linked to original sources

Compliance With Ecological Momentary Assessment Among Patients With Cancer: Systematic Review and Meta-Analysis.

BACKGROUND: Patients with cancer often experience substantial fluctuations in psychological states during disease management. Traditional research tools are limited in capturing these dynamic changes in real time, constraining clinicians' understanding of patients' true conditions. Ecological momentary assessment (EMA) enables high-frequency, real-time data collection, providing patient-reported data with greater ecological validity. However, the effectiveness of EMA studies critically depends on patient compliance, and reported compliance rates vary widely, with a lack of systematic quantitative synthesis. OBJECTIVE: This study aims to systematically review and quantitatively analyze compliance with EMA among patients with cancer, and to examine whether EMA design characteristics were associated with compliance. METHODS: Web of Science, PubMed, Embase, Cochrane Library, CINAHL, PsycINFO, CNKI, and Wanfang databases were searched for literature published up to April 30, 2026. Compliance was defined as completed prompts divided by delivered prompts. Single-group proportions were pooled using logit transformation and random-effects models with the Hartung-Knapp-Sidik-Jonkman adjustment. Prediction intervals were calculated to describe the expected distribution of compliance in future comparable settings. Subgroup analyses, univariable meta-regressions, leave-one-out sensitivity analyses, and tests for small-study effects were performed. Risk of bias was assessed using the Joanna Briggs Institute Critical Appraisal Checklist for Studies Reporting Prevalence Data, methodological reporting quality was assessed using a modified Checklist for Reporting EMA Studies, and certainty of evidence was evaluated using the Grading of Recommendations Assessment, Development, and Evaluation approach. RESULTS: Twenty-three studies involving 13,565 participants were included. The pooled compliance rate was 78.55% (95% CI 73.48%-82.87%), with a prediction interval of 48.59%-93.41%. Subgroup analyses identified no robust differences across study characteristics. Although study length showed a statistically significant subgroup test, the result was not stable after excluding singleton categories. Meta-regression analyses similarly found no significant linear associations for study length, prompts per day, items per prompt, or assessment window. Leave-one-out analyses showed that no single study drove the pooled estimate. Regarding the risk of bias, 2 studies were judged as low, while 21 were judged as moderate risk. Quality scores ranged from 6.5 to 9.0, and the certainty of evidence for the pooled compliance rate was rated as very low according to the Grading of Recommendations Assessment, Development, and Evaluation approach. CONCLUSIONS: Overall compliance with EMA among patients with cancer was moderate to high, suggesting that repeated real-world assessment may be feasible in oncology research settings. Nevertheless, the very high heterogeneity, wide prediction interval, and very low certainty of evidence indicate that compliance is context-dependent. The pooled estimate should therefore be interpreted as an approximate benchmark rather than a universal expected rate. Future oncology EMA studies should use standardized compliance denominators, report missing prompts transparently, and prospectively evaluate patient-centered design strategies that reduce burden while preserving data quality.

Humans↗

Involving older people in intermediate care.

BACKGROUND: Intermediate care has become a crucial part of the United Kingdom government's programme for improving services for older people. Older people comprise a substantial part of the user base for these services, and it is increasingly recognized that there is a need for greater user involvement in service development for intermediate care. National initiatives undertaken in intermediate care have sought to widen and deepen the remit of such services, and in this way promote greater independence and improved quality of care for older people. In particular, the government has set out clear plans for reshaping services for older people in the National Health Service Plan and the rationale for greater involvement of older people in service development. This article considers ways in which these national and local objectives may be achieved and considers some of the implications for nursing. AIM: This paper aims to explore the concept of intermediate care and to identify trends and existing evidence of user involvement in care. In this way it charts a possible way forward for the development of a more 'user sensitive' approach. METHOD: The following databases were searched: Medline, Cochrane Library, the Social Science Citation Index and CINAHL. Key words were 'intermediate care', 'older people', 'formal care', 'primary care', 'social services' and 'geriatrics', used in combination. FINDINGS: The findings from this study indicate that there is considerable scope for increased user involvement in service development for intermediate care. Such challenges may be more effectively met through greater clarity of the concept of intermediate care, and a bridging of user involvement at the practice and policy levels. Nurses are key providers of intermediate care in the community. CONCLUSIONS: The involvement of older people in intermediate care service development must be premised on a shared comprehension of the purpose and function of intermediate care. Nurses must be involved in shifting intermediate care from being service-focused to patient-centred. Effective participation eschews the application of global constructs for older people, while supporting greater participation at all levels and robust implementation processes.

Aged↗

Antistreptococcal interventions for guttate and chronic plaque psoriasis.

BACKGROUND: Guttate psoriasis is a distinctive acute form of psoriasis which characteristically occurs in children and young adults. It is closely associated with preceding streptococcal sore throat or tonsillitis. Some authorities have claimed that ordinary (chronic plaque) psoriasis may also be made worse by infection at distant sites. Although many dermatologists have recommended using antibiotics for guttate psoriasis in particular, it is not clear whether they influence the course of either form of psoriasis. Some dermatologists have also recommended tonsillectomy for psoriasis in patients with recurrent streptococcal sore throat. OBJECTIVES: To assess the evidence for effectiveness of antistreptococcal interventions including antibiotics and tonsillectomy in the management of acute guttate and chronic plaque psoriasis. SEARCH STRATEGY: We searched the Cochrane Clinical Trials Register (Cochrane Library, Issue 3, 1999), Medline (1966- September 1999), Embase (1988-September 1999), the Salford Database of Psoriasis Trials (to November 1999) and the European Dermato-Epidemiology Network (EDEN) Psoriasis Trials Database (to November 1999) for terms [STREPTOCOCC* or ANTIBIOTIC* or TONSIL*] and PSORIASIS using the Cochrane Skin Group search strategy. SELECTION CRITERIA: Randomised trials of one or more antistreptococcal interventions in patients with guttate or chronic plaque psoriasis. DATA COLLECTION AND ANALYSIS: Two reviewers independently examined each retrieved trial for eligibility and quality. MAIN RESULTS: The one eligible trial we identified compared the use of two oral antibiotic schedules in 20 psoriasis patients, predominantly of guttate type, who had evidence of beta-haemolytic streptococcal colonisation. Either rifampicin or placebo was added to the end of a standard course of antistreptococcal antibiotic (phenoxymethylpenicillin or erythromycin). No patient in either arm of the study improved during the observation period. No randomised trials of tonsillectomy for psoriasis were identified. REVIEWER'S CONCLUSIONS: Although it is well known that guttate psoriasis may be precipitated by streptococcal infection, there is no firm evidence to support the use of antibiotics either in the management of established guttate psoriasis or in preventing the development of guttate psoriasis following streptococcal sore throat. Although both antibiotics and tonsillectomy have frequently been advocated for patients with recurrent guttate psoriasis or chronic plaque psoriasis, there is to date no good evidence that either intervention is beneficial.

Anti-Bacterial Agents↗

TreeDyn: towards dynamic graphics and annotations for analyses of trees.

BACKGROUND: Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptions or gene functions that can hardly be encoded within the tree itself (if using popular tree formats). Consequently, a tedious manual analysis and post-processing of the tree graphics are required if one needs to use external information for displaying or investigating trees. RESULTS: We have developed TreeDyn, a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees. CONCLUSION: TreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections.

Computer Graphics↗

Comparison of antiproliferative effects of experimental and established antipsoriatic drugs on human keratinocytes, using a simple 96-well-plate assay.

Pharmacological treatments for psoriasis are generally based on antiproliferative, anti-inflammatory, or differentiation-modifying activity, or a combination of two or more of these actions. Potentially new drugs for treatment of psoriasis, which act on proliferation, can be identified by screening large compound libraries in a cell proliferation model that allows for characterization of drug effects on in vitro growth of normal human keratinocytes. High-throughput programs based on biological testing of diverse collections of compounds can rapidly identify leads for potential drug candidates in the treatment of psoriasis. In this study, we describe nonradioactive measurement of keratinocyte proliferation in the exponential growth phase in a 96-well format, using a sensitive deoxyribonucleic acid-binding dye to analyze drugs that are pharmacologically active in growth inhibition. Release of lactate dehydrogenase was used to exclude cytotoxic effects. We examined a number of compounds in a test range of 10(-7) to 10(-5) M, including known antipsoriatic drugs, and experimental drugs that are potentially useful in the treatment of psoriasis. We found strong concentration-dependent growth inhibition by dithranol, an antipsoriatic compound that is presumed to target the epidermal compartment. Methotrexate, cyclosporin A, and all-trans retinoic acid did not significantly affect proliferation at therapeutically relevant concentrations. The p38 mitogen-activated protein kinase inhibitor, SB220025, and curcumin, a natural phytochemical, inhibited keratinocyte proliferation at 10(-5) M. We conclude that this assay, in combination with the previously developed assays for psoriatic differentiation, provides a useful tool for identification of antipsoriatic drugs.

Anthralin↗

Single-chain Fv antibody with specificity for Listeria monocytogenes.

Single chain antibodies (scFv) exhibiting specific binding to Listeria monocytogenes strains were isolated from a pool of random scFvs expressed on the surface of filamentous bacteriophages. Positive selection (panning) using L. monocytogenes was used to enrich for phage clones with the desired binding affinity, and negative selection using L. innocua and L. ivanovii was used to remove phages expressing cross-reactive antibody fragments. A single phage clone, P4:A8, was selected using two independent panning schemes. A rapid assay was devised to determine phage antibody binding specificity and was used to develop a selectivity profile for individual phage clones. The P4:A8 clone was screened against a panel of bacteria consisting of eight strains of L. monocytogenes, one each of the other six species of Listeria and nine other relevant bacterial species. A collection of individual clones from the penultimate panning was also screened against a subset of the panel of bacteria. The selectivity profiles indicate that multiple clones, including P4:A8, exhibit binding to one or more strains of L. monocytogenes without cross-reactivity toward any other species in the panel. This is the first report of a species-specific antibody for viable cells of L. monocytogenes (i.e., the ability to bind to L. monocytogenes without cross-reactivity toward any other species of Listeria).

Antibodies, Bacterial↗

Sal-Site: integrating new and existing ambystomatid salamander research and informational resources.

Salamanders of the genus Ambystoma are a unique model organism system because they enable natural history and biomedical research in the laboratory or field. We developed Sal-Site to integrate new and existing ambystomatid salamander research resources in support of this model system. Sal-Site hosts six important resources: 1) Salamander Genome Project: an information-based web-site describing progress in genome resource development, 2) Ambystoma EST Database: a database of manually edited and analyzed contigs assembled from ESTs that were collected from A. tigrinum tigrinum and A. mexicanum, 3) Ambystoma Gene Collection: a database containing full-length protein-coding sequences, 4) Ambystoma Map and Marker Collection: an image and database resource that shows the location of mapped markers on linkage groups, provides information about markers, and provides integrating links to Ambystoma EST Database and Ambystoma Gene Collection databases, 5) Ambystoma Genetic Stock Center: a website and collection of databases that describe an NSF funded salamander rearing facility that generates and distributes biological materials to researchers and educators throughout the world, and 6) Ambystoma Research Coordination Network: a web-site detailing current research projects and activities involving an international group of researchers. Sal-Site is accessible at http://www.ambystoma.org.

Animals↗

Antibiotics for preventing infection in open limb fractures.

BACKGROUND: Wound and bone infections are frequently associated with open fractures of the extremities and may add significantly to the resulting morbidity. The administration of antibiotics is routinely used in developed countries as an adjunct to a comprehensive management protocol that also includes irrigation, surgical debridement and stabilisation when indicated, and is thought to reduce the frequency of infections. OBJECTIVES: To quantify the evidence for the effectiveness of antibiotics in the initial treatment of open fractures of the limbs. SEARCH STRATEGY: We searched the Cochrane Musculoskeletal Injuries Group specialised register (April 2003), the Cochrane Central Register of Controlled Trials (The Cochrane Library issue 1, 2003), MEDLINE (1966 to April 2003), EMBASE (1988 to April 2003), LILACS (1992 to June 2002) and reference lists of articles. Proceedings of meetings of the American Academy of Orthopaedic Surgeons (1980 to 2001), the Orthopaedic Trauma Association (1990 to 2001) and the Société Internationale de Chirurgie Orthopedique et Traumatologique (1980 to 2001) were hand searched. We also contacted published researchers in the field. SELECTION CRITERIA: Randomised or quasi-randomised controlled trials involving: participants - people of any age with open fractures of the limbs; intervention - antibiotic administered before or at the time of primary treatment of the open fracture compared with placebo or no antibiotic; outcome measures - early wound infection, chronic drainage, acute or chronic osteomyelitis, delayed unions or non-unions, amputations and deaths. DATA COLLECTION AND ANALYSIS: Two reviewers independently screened papers for inclusion, assessed trial quality using an eight item scale, and extracted data. Additional information was sought from three trialists. Pooled data are presented graphically. MAIN RESULTS: Data from 913 participants in seven studies were analysed. The use of antibiotics had a protective effect against early infection compared with no antibiotics or placebo (relative risk 0.41 (95% confidence interval (CI) 0.27 to 0.63); absolute risk reduction 0.08 (95% CI 0.04 to 0.12); NNT 13 (95% CI 8 to 25)). There were insufficient data in the included studies to evaluate other outcomes. REVIEWER'S CONCLUSIONS: Antibiotics reduce the incidence of early infections in open fractures of the limbs. Further placebo controlled randomised trials are unlikely to be justified in middle and high income countries. Further research is necessary to the determine the avoidable burden of morbidity in countries where antibiotics are not used routinely in the management of open fractures.

Antibiotic Prophylaxis↗

Antibiotic regimens for secondary peritonitis of gastrointestinal origin in adults.

BACKGROUND: Secondary peritonitis is associated with a high mortality rate and if not treated successfully leads to development of abscesses, severe sepsis and multi-organ failure. Source control and adjunctive antibiotics are the mainstay of treatment. However, no conclusive evidence suggest that one antibiotic regimen is better than any other but at the same time have a lower toxicity. OBJECTIVES: To ascertain the efficacy and adverse effects of different antibiotic regimens in treating intra-abdominal infections in adults. Outcomes were divided into primary (clinical success and effectiveness in reducing mortality) and secondary (microbiological success, preventing wound infection, intra-abdominal abscess, clinical sepsis, remote infection, superinfection, adverse reactions, duration of treatment required, effectiveness in reducing hospitalised stay, and time to defervescence). SEARCH STRATEGY: We searched the Cochrane Central Register of Controlled Trials (CENTRAL) (Cochrane Library, Issue 4, 2004), MEDLINE (from 1966 to November 2004), EMBASE (from 1980 to November 2004) and Cochrane Colorectal Cancer Group specialised register SR-COLOCA. Bibliographies of identified studies were screened for further relevant trials. SELECTION CRITERIA: Randomised and quasi-randomised controlled trials comparing different antibiotic regimens in the treatment of secondary peritonitis in adults were selected. Trials reporting gynaecological or traumatic peritonitis were excluded from this review. Ambiguity regarding suitability of trials were discussed among the review team. DATA COLLECTION AND ANALYSIS: Six reviewers independently assessed trial quality and extracted data. Data collection was standardised using data collection form to ensure uniformity among reviewers. Statistical analyses were performed using the random effects model and the results expressed as odds ratio for dichotomous outcomes, or weight mean difference for continuous data with 95% confidence intervals. MAIN RESULTS: Fourty studies with 5094 patients met the inclusion criteria. Sixteen different comparative antibiotic regimens were reported. All antibiotics showed equivocal comparability in terms of clinical success. Mortality did not differ between the regimens. Despite the potential high toxicity profile of regimens using aminoglycosides, this was not demonstrated in this review. The reason for this could be the inherent bias within clinical trials in the form of patient selection and stringency in monitoring drug levels. AUTHORS' CONCLUSIONS: No specific recommendations can be made for the first line treatment of secondary peritonitis in adults with antibiotics, as all regimens showed equivocal efficacy. Other factors such as local guidelines and preferences, ease of administration, costs and availability must therefore be taken into consideration in deciding the antibiotic regimen of choice. Future trials should attempt to stratify patients and perform intention-to-treat analysis to allow better external validity.

Anti-Bacterial Agents↗

Amniotomy plus intravenous oxytocin for induction of labour.

BACKGROUND: Induction of labour is a common obstetric intervention. Amniotomy alone for induction of labour is reviewed separately and oxytocin alone for induction of labour is being prepared for inclusion in The Cochrane Library. This review will address the use of the combination of these two methods for induction of labour in the third trimester. This is one of a series of reviews of methods of cervical ripening and labour induction using standardised methodology. OBJECTIVES: To determine, from the best available evidence, the efficacy and safety of amniotomy and intravenous oxytocin for third trimester induction of labour. SEARCH STRATEGY: The Cochrane Pregnancy and Childbirth Group Trials Register, the Cochrane Controlled Trials Register and reference lists of articles were searched. Date of last search: May 2001. SELECTION CRITERIA: The criteria for inclusion included the following: (1) clinical trials comparing amniotomy plus intravenous oxytocin used for third trimester cervical ripening or labour induction with placebo/no treatment or other methods listed above it on a predefined list of labour induction methods; (2) random allocation to the treatment or control group; (3) adequate allocation concealment; (4) violations of allocated management not sufficient to materially affect conclusions; (5) clinically meaningful outcome measures reported; (6) data available for analysis according to the random allocation; (7) missing data insufficient to materially affect the conclusions. DATA COLLECTION AND ANALYSIS: Trial quality assessment and data extraction were done by both reviewers. A strategy was developed to deal with the large volume and complexity of trial data relating to labour induction. This involved a two-stage method of data extraction. The initial data extraction was done centrally, and incorporated into a series of primary reviews arranged by methods of induction of labour, following a standardised methodology. The data is to be extracted from the primary reviews into a series of secondary reviews, arranged by category of woman. MAIN RESULTS: Seventeen trials involving 2566 women were included. Amniotomy and intravenous oxytocin were found to result in fewer women being undelivered vaginally at 24 hours than amniotomy alone (relative risk (RR) 0.03, 95% confidence intervals (CI) 0.001-0.49). This finding was based on the results of a single study of 100 women. As regards secondary results amniotomy and intravenous oxytocin resulted in significantly fewer instrumental vaginal deliveries than placebo (RR 0.18, CI 0.05-0.58). Amniotomy and intravenous oxytocin resulted in more postpartum haemorrhage than vaginal prostaglandins (RR 5.5, CI 1.26-24.07). Significantly more women were also dissatisfied with amniotomy and intravenous oxytocin when compared with vaginal prostaglandins, RR 53, CI 3.32-846.51. REVIEWER'S CONCLUSIONS: Data on the effectiveness and safety of amniotomy and intravenous oxytocin are lacking. No recommendations for clinical practice can be made on the basis of this review. Amniotomy and intravenous oxytocin is a combination of two methods of induction of labour and both methods are utilised in clinical practice. If their use is to be continued it is important to compare the effectiveness and safety of these methods, and to define under which clinical circumstances one may be preferable to another.

Amnion↗

Physical measures for treating depression in dialysis patients.

BACKGROUND: Depression is the most common psychological problem in the chronic dialysis population. The diagnosis of depression in patients on chronic dialysis is confounded by the fact that several symptoms of uraemia mimic the somatic components of depression. It affects their physical, psychological and social well-being. Furthermore, the frequent occurrence of cardiovascular problems and the pharmacokinetic consequences of renal impairment may make drug treatment of depression difficult. OBJECTIVES: The aim of this systematic review was to assess the efficacy and safety of physical measures in the treatment of depression in patients who are dialysed for end-stage renal disease. SEARCH STRATEGY: A comprehensive search strategy was employed to identify all Randomised Controlled Trials (RCTs) relevant to the treatment of depression in patients on chronic dialysis. The following database were searched - MEDLINE (1966-March 2004), EMBASE (1980-March 2004), PSYCHINFO (1872-March 2004), The Cochrane Library (Issue 1, 2004). Authors of included studies were contacted, reference lists of identified RCTs and relevant narrative reviews were screened. SELECTION CRITERIA: RCTs comparing drugs with placebo or no treatment, or a comparison of drugs against a combination of electroconvulsive therapy and drugs. DATA COLLECTION AND ANALYSIS: Data were abstracted by two investigators independently onto a standard form and subsequently entered into Review Manager 4.2. Relative risk (RR) for dichotomous data and a (weighted) mean difference (WMD) for continuous data were calculated with 95% confidence intervals (95% CI). MAIN RESULTS: Only one trial, with a total of 12 patients and of eight weeks duration was identified. The trial compared fluoxetine against placebo in depressed patients on chronic dialysis. This study did not show any significant difference in depression scores between the treatment and control groups or safety. AUTHORS' CONCLUSIONS: Firm conclusions on the efficacy of physical methods of treatment cannot be made as we identified only one small RCT that was of short duration. More larger and longer term RCTs are needed in this area. Current screening tools for depression are recognised to have poor specificity in the medically ill due to overlap of somatic symptoms of the medical illness. The development of a valid diagnostic tool would be helpful.

Depression↗

[Resources of information in the field of bioethics in Italy: survey of the present state and perspectives].

The research project "Collection and dissemination of bioethical information through an integrated electronic system", started in 2001 by the Istituto Superiore di Sanità (ISS), had among its objectives, the realization of an integrated system for data collection and exchange of documents related to bioethics. The system should act as a reference tool for those research activities impacting on citizens' health and welfare. This paper aims at presenting some initiatives, developed in the project framework, in order to establish an Italian documentation network, among which: a) exchange of ISS publications with Italian institutions active in this field; b) survey through a questionnaire aimed at assessing Italian informative resources, state-of-the-art and holdings of documentation centres and ethical committees; c) Italian Internet resources analysis. The results of the survey, together with the analysis of web sites, show that at present in Italy there are many interesting initiatives for collecting and spreading of documentation in the bioethical fields, but there is an urgent need for an integration of such resources. Ethical committees generally speaking need a larger availability of documents, while there are good potentialities for the establishment of an electronic network for document retrieval and delivery.

Academies and Institutes↗

Preliminary profile of the Cryptosporidium parvum genome: an expressed sequence tag and genome survey sequence analysis.

Cryptosporidium parvum is a protozoan enteropathogen that infects humans and animals and causes a pronounced diarrheal disease that can be life-threatening in immunocompromised hosts. No specific chemo- or immunotherapies exist to treat cryptosporidiosis and little molecular information is available to guide development of such therapies. To accelerate gene discovery and identify genes encoding potential drug and vaccine targets we constructed sporozoite cDNA and genomic DNA sequencing libraries from the Iowa isolate of C. parvum and determined approximately 2000 sequence tags by single-pass sequencing of random clones. Together, the 567 expressed sequence tags (ESTs) and 1507 genome survey sequences (GSSs) totaled one megabase (1 mb) of unique genomic sequence indicating that approximately 10% of the 10.4 mb C. parvum genome has been sequence tagged in this gene discovery expedition. The tags were used to search the public nucleic acid and protein databases via BLAST analyses, and 180 ESTs (32%) and 277 GSSs (18%) exhibited similarity with database sequences at smallest sum probabilities P(N)< or =10(-8). Some tags encoded proteins with clear therapeutic potential including S-adenosylhomocysteine hydrolase, histone deacetylase, polyketide/fatty-acid synthases, various cyclophilins, thrombospondin-related cysteine-rich protein and ATP-binding-cassette transporters. Several anonymous ESTs encoded proteins predicted to contain signal peptides or multiple transmembrane spanning segments suggesting they were destined for membrane-bound compartments, the cell surface or extracellular secretion. One-hundred four simple sequence repeats were identified within the nonredundant sequence tag collection with (TAA)(> or =6)/(TTA)(> or =6) and (TA)(> or = 10)/(AT)(> or =10 ) being the most prevalent, occurring 40 and 15 times, respectively. Various cellular RNAs and their genes were also identified including the small and large ribosomal RNAs, five tRNAs, the U2 small nuclear RNA, and the small and large virus-like, double-stranded RNAs. This investigation has demonstrated that survey sequencing is an efficient procedure for gene discovery and genome characterization and has identified and sequence tagged many C. parvum genes encoding potential therapeutic targets.

Amino Acid Sequence↗

Moss (Physcomitrella patens) functional genomics--Gene discovery and tool development, with implications for crop plants and human health.

Recently, the moss Physcomitrella patens was established as a versatile tool in plant functional genomics. Mosses represent the oldest living clade of land plants, separated by approximately 450 million years of evolution from crop plants. Consequently, mosses contain metabolites and genes not known from these seed plants. In Physcomitrella, nuclear genes can be targeted by homologous recombination as efficiently as in yeast, allowing reverse genetics approaches in plants at high-throughput levels for the first time. Comprehensive expressed sequence tag databases gave new insights into the levels of diversity in land plants which are now ready to be exploited in plant biotechnology. In forward genetics screens, saturated tagged mutant collections help to unravel novel gene - function relationships. Additionally, proteomics tools are at hand to analyse subcellular proteomes, as well as the phosphoproteome, as the core of eukaryotic signal transduction. Moreover, specifically designed Physcomitrella strains can produce human therapeutic proteins safely and cost-effectively in bioreactors.

Bioreactors↗

Expressed sequence tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis.

The process of embryogenesis in gymnosperms differs in significant ways from the more widely studied process in angiosperms. To further our understanding of embryogenesis in gymnosperms, we have generated Expressed Sequence Tags (ESTs) from four cDNA libraries constructed from un-normalized, normalized, and subtracted RNA populations of zygotic and somatic embryos of loblolly pine (Pinus taeda L.). A total of 68,721 ESTs were generated from 68,131 cDNA clones. Following clustering and assembly, these sequences collapsed into 5,274 contigs and 6,880 singleton sequences for a total of 12,154 non-redundant sequences. Searches of a non-identical amino acid database revealed a putative homolog for 9,189 sequences, leaving 2,965 sequences with no known function. More extensive searches of additional plant sequence data sets revealed a putative homolog for all but 1,388 (11.4%) of the sequences. Using gene ontologies, a known function could be assigned for 5,495 of the 12,154 total non-redundant sequences with 13,633 associations in total assigned. When compared to approximately 72,000 sequences in a collated P. taeda transcript assembly derived from >245,000 ESTs derived from root, xylem, stem, needles, pollen cone, and shoot ESTs, 3,458 (28.5%) of the non-redundant embryo sequences were unique and thereby provide a valuable addition to development of a complete loblolly pine transcriptome. To assess similarities between angiosperm and gymnosperm embryo development, we examined our EST collection for putative homologs of angiosperm genes implicated in embryogenesis. Out of 108 angiosperm embryogenesis-related genes, homologs were present for 83 of these genes suggesting that pine contains similar genes for embryogenesis and that our RNA sampling methods were successful. We also identified sequences from the pine embryo transcriptome that have no known function and may contribute to the programming of gene expression and embryo development.

Amino Acid Sequence↗

[Optimizing history taking for evaluating the risk of venous thromboembolism: the OPTIMEV study].

UNLABELLED: Venous thromboembolism (VTE) is a frequent disease and remains a major cause of mortality and morbidity among our patients. During the 20 past years, clinical description, diagnostic tools, and treatment have changed dramatically. Most published data describing risk factors for VTE no longer apply to the patients seen in daily practice. We present here the rationale, aims, and methodology of the OPTIMEV Study (OPTimisation de l'Interrogatoire pour la Maladie thromboEmbolique Veineuse). RATIONALE: Risk factors for VTE are numerous, complex and interactions between them and their clinical importance is difficult to measure (table I). For example, odds ratios for VTE recurrence vary greatly across longitudinal studies. We searched the National Library of Medecine (PubMed) and the Amedeo website using the following keywords: "venous thromboembolism", "pulmonary embolism", "deep vein thrombosis", "risk factors". We selected 84 relevant articles published between 1972 and 2005. Based on this literature analysis, we identified the following major risk factors: VTE recurrence, surgery, cancer, immobilization, age, biological factors. For these factors, data are lacking and some questions are proposed. OBJECTIVES: The broad objective of the study is to better evaluate clinical risk factors that fit today's practice against VTE. Specific aims are: 1) to determine whether risk factors are different between proximal and distal deep vein thrombosis (DVT); 2) to develop and prospectively validate a new prediction rule for outpatients. The primary hypothesis is that careful assessment of VTE recurrence, adequate surgical thromboprophylaxis, cancer staging, and varicose vein stratification according to the CEAP classification, is mandatory for accurate evaluation of thromboembolic disease risk. METHODS: We conducted a multicenter, prospective, cohort study of 10000 patients. Enrollees are inpatients and outpatients presenting with a clinical suspicion of VTE in Emergency Departments and outpatient clinics in France. 4173 patients have been enrolled at this time (Figure 2). All eligible patients are enrolled during a selected period of time through different seasons. Data are collected by physicians in charge of the patients using an electronic case recording form. Collected data include baseline characteristics, risk factors, results of diagnostic investigations. Outcome measures obtained through telephone interview at 3 and 12 months include cancer diagnosis, VTE recurrence, haemorrhagic events, treatments, death. Univariate and multivariate analysis will be performed using multilevel logistic regression. The study organization is performed by the Centre d'Investigation Clinique de Grenoble and is sponsored by the French Society of Vascular Medicine. First results, to be published in 2006, will allow development of new prediction rules for VTE diagnosis.

Age Factors↗

Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods.

BACKGROUND: Rice blast, caused by the fungal pathogen Magnaporthe grisea, is a devastating disease causing tremendous yield loss in rice production. The public availability of the complete genome sequence of M. grisea provides ample opportunities to understand the molecular mechanism of its pathogenesis on rice plants at the transcriptome level. To identify all the expressed genes encoded in the fungal genome, we have analyzed the mycelium and appressorium transcriptomes using massively parallel signature sequencing (MPSS), robust-long serial analysis of gene expression (RL-SAGE) and oligoarray methods. RESULTS: The MPSS analyses identified 12,531 and 12,927 distinct significant tags from mycelia and appressoria, respectively, while the RL-SAGE analysis identified 16,580 distinct significant tags from the mycelial library. When matching these 12,531 mycelial and 12,927 appressorial significant tags to the annotated CDS, 500 bp upstream and 500 bp downstream of CDS, 6,735 unique genes in mycelia and 7,686 unique genes in appressoria were identified. A total of 7,135 mycelium-specific and 7,531 appressorium-specific significant MPSS tags were identified, which correspond to 2,088 and 1,784 annotated genes, respectively, when matching to the same set of reference sequences. Nearly 85% of the significant MPSS tags from mycelia and appressoria and 65% of the significant tags from the RL-SAGE mycelium library matched to the M. grisea genome. MPSS and RL-SAGE methods supported the expression of more than 9,000 genes, representing over 80% of the predicted genes in M. grisea. About 40% of the MPSS tags and 55% of the RL-SAGE tags represent novel transcripts since they had no matches in the existing M. grisea EST collections. Over 19% of the annotated genes were found to produce both sense and antisense tags in the protein-coding region. The oligoarray analysis identified the expression of 3,793 mycelium-specific and 4,652 appressorium-specific genes. A total of 2,430 mycelial genes and 1,886 appressorial genes were identified by both MPSS and oligoarray. CONCLUSION: The comprehensive and deep transcriptome analysis by MPSS and RL-SAGE methods identified many novel sense and antisense transcripts in the M. grisea genome at two important growth stages. The differentially expressed transcripts that were identified, especially those specifically expressed in appressoria, represent a genomic resource useful for gaining a better understanding of the molecular basis of M. grisea pathogenicity. Further analysis of the novel antisense transcripts will provide new insights into the regulation and function of these genes in fungal growth, development and pathogenesis in the host plants.

DNA, Fungal↗

Epilepsy clinics versus general neurology or medical clinics.

BACKGROUND: Epilepsy is the most common serious neurological condition after stroke, with a 0.5 per cent prevalence, and a two to three per cent life time risk of being given a diagnosis of epilepsy in the developed world. As a result of perceived deficiencies of the quality of care offered to people with epilepsy, two models of service provision have been suggested by researchers: specialist epilepsy out-patient clinics (as opposed to the management of patients in general neurology clinics or general medical clinics) and nurse-based liaison services between primary (GP) and secondary/tertiary (hospital based) care. OBJECTIVES: The aim of this review was to overview the evidence from controlled trials investigating the effectiveness of specialist epilepsy clinics compared to routine care. A second similar review investigating the effectiveness of specialist epilepsy nurses is also underway. SEARCH STRATEGY: We searched the Cochrane Epilepsy Group trials register, the Cochrane Controlled Trials Register (Cochrane Library Issue 4, 1999), MEDLINE (January 1966 to December 1999), GEARS, BIDS (EMBASE=Excepta Medica(1998-99)), ECRI, Effectiveness Healthcare Bulletin, Effectiveness Matters, Bandolier, Evidence Based Purchasing, National Research Register, Vignettes and expert panels from Standing Group on Health Technology Assessment, PsycLit database, World Wide Web sites and reference lists of articles. In addition, we contacted experts in the field. SELECTION CRITERIA: All randomized controlled and quasi-randomized trials which considered specialist epilepsy clinic interventions with standard or alternative care were included in this review. DATA COLLECTION AND ANALYSIS: No controlled trials of suitable quality were identified for inclusion in the review. MAIN RESULTS: No controlled trials of suitable quality were identified for inclusion in the review. REVIEWER'S CONCLUSIONS: It is not known whether specialist epilepsy clinics improve outcomes for people with epilepsy. As yet, there is no high quality evidence which describes their effectiveness in improving care for people with epilepsy.

Epilepsy↗