SEARCH · Search PubMed
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.
The emerging clinical importance of staphylococcal infections prompted us to establish a reference database for partial RNA polymerase B (rpoB; nucleotides 1444-1928) gene sequences from type strains of all staphylococcal species and subspecies. This database correctly identified 55 clinical staphylococcal isolates; all were correctly identified at the species level. At the subspecies level, rpoB misidentified only 2 isolates.
We analyzed retrospectively the use of Physician Desk Reference Database searches to identify epidemics of tularemia, nephropathy, Pogosta disease, and Lyme disease and compared the searches with mandatory laboratory reports to the National Infectious Diseases Register in Finland during 1995. Continuous recording of such searches may be a tool for early detection of epidemics.
Several quantitative bull's-eye database programs have been developed and employed successfully, but generally they restrict the user to limited types of quantitative analysis. We developed a type of bull's-eye analysis which facilitates user-defined processing, and then explored the effects of various types of processing on the comparisons of patient information with that of reference databases. Male and female bull's-eye database were generated from 32 normal patients using unweighted 2D prefiltering, ramp backprojection, unweighted 3D postfiltering, and peak value circumferential plotting (base method). The data from each patient were then reprocessed and compared to the databases by means of three different approaches: (1) using the base method, (2) using average as opposed to peak value profiles, and (3) using a resolution recovery prefilter instead of a smoothing prefilter. Significant differences in the number of apparently abnormal regions were found between the three methods. In other words, the type of single-photon emission tomography (SPET) processing affected the accuracy of comparisons between patient and database information. Because even sophisticated analysis can now be performed on personal computers, we conclude that, rather than a preprocessed data file, clinical "normal reference" information should consist of original SPET data (in a standard format, e.g., Interfile) from a series of documented normal patients. Each user could then generate reference bull's-eye database by applying his or her own clinical processing procedures to the data.
OBJECTIVES: To summarize the effects of garlic on several cardiovascular-related factors and to note its adverse effects. METHODS: English and non-English citations were identified from 11 electronic databases, references, manufacturers, and experts from January 1966 through February 2000 (depending on the database searched). Reports of cardiovascular-related effects were limited to randomized controlled trials lasting at least 4 weeks. Reports of adverse effects were not limited by study design. From 1798 pertinent records, 45 randomized trials and 73 additional studies reporting adverse events were identified. Two physicians abstracted outcomes and assessed adequacy of randomization, blinding, and handling of dropouts. Standardized mean differences of lipid outcomes from placebo-controlled trials were adjusted for baseline differences and pooled using random effects methods. RESULTS: Compared with placebo, garlic preparations may lead to small reductions in the total cholesterol level at 1 month (range of average pooled reductions, 0.03-0.45 mmol/L [1.2-17.3 mg/dL]) and at 3 months (range of average pooled reductions 0.32-0.66 mmol/L [12.4-25.4 mg/dL]), but not at 6 months. Changes in low-density lipoprotein levels and triglyceride levels paralleled total cholesterol level results; no statistically significant changes in high-density lipoprotein levels were observed. Trials also reported significant reductions in platelet aggregation and mixed effects on blood pressure outcomes. No effects on glycemic-related outcomes were found. Proven adverse effects included malodorous breath and body odor. Other unproven effects included flatulence, esophageal and abdominal pain, allergic reactions, and bleeding. CONCLUSIONS: Trials suggest possible small short-term benefits of garlic on some lipid and antiplatelet factors, insignificant effects on blood pressure, and no effect on glucose levels. Conclusions regarding clinical significance are limited by the marginal quality and short duration of many trials and by the unpredictable release and inadequate definition of active constituents in study preparations.
MOTIVATION: Based on a gene classification into hierarchical categories ('BINs'), MapMan was originally developed to display Arabidopsis thaliana gene expression in a functional context. We have created a bioinformatics system to extend MapMan to any organism by using a new BIN structure based on the KEGG database. Gene sequences are assigned to this ontology by homology relationships in four reference databases: KEGG, COG, Swiss-Prot and Gene Ontology. We applied this system to tailor MapMan to the GeneChips of two model legumes, Glycine max and Medicago truncatula. We also developed a module to identify the most relevant pathways involved. AVAILABILITY: All mapping files, pathway pictures and the analysis method are available at http://bioinfoserver.rsbs.anu.edu.au/
BACKGROUND: We present a complete re-implementation of the segment-based approach to multiple protein alignment that contains a number of improvements compared to the previous version 2.2 of DIALIGN. This previous version is superior to Needleman-Wunsch-based multi-alignment programs on locally related sequence sets. However, it is often outperformed by these methods on data sets with global but weak similarity at the primary-sequence level. RESULTS: In the present paper, we discuss strengths and weaknesses of DIALIGN in view of the underlying objective function. Based on these results, we propose several heuristics to improve the segment-based alignment approach. For pairwise alignment, we implemented a fragment-chaining algorithm that favours chains of low-scoring local alignments over isolated high-scoring fragments. For multiple alignment, we use an improved greedy procedure that is less sensitive to spurious local sequence similarities. To evaluate our method on globally related protein families, we used the well-known database BAliBASE. For benchmarking tests on locally related sequences, we created a new reference database called IRMBASE which consists of simulated conserved motifs implanted into non-related random sequences. CONCLUSION: On BAliBASE, our new program performs significantly better than the previous version of DIALIGN and is comparable to the standard global aligner CLUSTAL W, though it is outperformed by some newly developed programs that focus on global alignment. On the locally related test sets in IRMBASE, our method outperforms all other programs that we evaluated.
This work comprises lists of publications and computer data bases available at the Scientific Information Department, The Nofer Institute of Occupational Medicine, Lodz, Poland, containing information on cancer risks resulting from exposure to carcinogenic agents. The following publications have been described: IARC Monographs on the Evaluation of Carcinogenic Risk to Humans; Official lists of carcinogens valid in individual countries; a periodical--Survey of compounds which have been tested for carcinogenic activity; a guide--The Annual Report on Carcinogens, a series on Carcinogens in the Occupational Environment, comprising Information Cards and Monographs; a guide on Carcinogenic Agents, and computer databases, including the INCAR, IRIS, IRPTC, RTECS CHEMINFO factual databases and the CANCER-CD, MEDLINE, TOXLINE, NIOSHTIC and MEDIP bibliographic (or reference) databases. The presented publications and databases may prove helpful in searching for data on identifying and preventing the adverse health effects of environmental and occupational exposure to carcinogens.
A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the interaction network. However, the necessary data integration across experiments is currently hampered by the fragmentation of publicly available protein interaction data, which exists in different formats in databases, on authors' websites or sometimes only in print publications. Here, we propose a community standard data model for the representation and exchange of protein interaction data. This data model has been jointly developed by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO), and is supported by major protein interaction data providers, in particular the Biomolecular Interaction Network Database (BIND), Cellzome (Heidelberg, Germany), the Database of Interacting Proteins (DIP), Dana Farber Cancer Institute (Boston, MA, USA), the Human Protein Reference Database (HPRD), Hybrigenics (Paris, France), the European Bioinformatics Institute's (EMBL-EBI, Hinxton, UK) IntAct, the Molecular Interactions (MINT, Rome, Italy) database, the Protein-Protein Interaction Database (PPID, Edinburgh, UK) and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING, EMBL, Heidelberg, Germany).
With the accelerated accumulation of genomic sequence data, there is a pressing need to develop computational methods and advanced bioinformatics infrastructure for reliable and large-scale protein annotation and biological knowledge discovery. The Protein Information Resource (PIR) provides an integrated public resource of protein informatics to support genomic and proteomic research. PIR produces the Protein Sequence Database of functionally annotated protein sequences. The annotation problems are addressed by a classification-driven and rule-based method with evidence attribution, coupled with an integrated knowledge base system being developed. The approach allows sensitive identification, consistent and rich annotation, and systematic detection of annotation errors, as well as distinction of experimentally verified and computationally predicted features. The knowledge base consists of two new databases, sequence analysis tools, and graphical interfaces. PIR-NREF, a non-redundant reference database, provides a timely and comprehensive collection of all protein sequences, totaling more than 1,000,000 entries. iProClass, an integrated database of protein family, function, and structure information, provides extensive value-added features for about 830,000 proteins with rich links to over 50 molecular databases. This paper describes our approach to protein functional annotation with case studies and examines common identification errors. It also illustrates that data integration in PIR supports exploration of protein relationships and may reveal protein functional associations beyond sequence homology.
MOTIVATION: The use or study of chemical compounds permeates almost every scientific field and in each of them, the amount of textual information is growing rapidly. There is a need to accurately identify chemical names within text for a number of informatics efforts such as database curation, report summarization, tagging of named entities and keywords, or the development/curation of reference databases. RESULTS: A first-order Markov Model (MM) was evaluated for its ability to distinguish chemical names from words, yielding approximately 93% recall in recognizing chemical terms and approximately 99% precision in rejecting non-chemical terms on smaller test sets. However, because total false-positive events increase with the number of words analyzed, the scalability of name recognition was measured by processing 13.1 million MEDLINE records. The method yielded precision ranges from 54.7% to 100%, depending upon the cutoff score used, averaging 82.7% for approximately 1.05 million putative chemical terms extracted. Extracted chemical terms were analyzed to estimate the number of spelling variants per term, which correlated with the total number of times the chemical name appeared in MEDLINE. This variability in term construction was found to affect both information retrieval and term mapping when using PubMed and Ovid.
INTRODUCTION: While osteoporosis is common among women of Chinese descent, a readily available bone mineral density (BMD) referent database for Chinese American women does not exist. Fracture risk among this population is currently assessed using a Caucasian reference as well as diagnostic criteria for osteoporosis developed for postmenopausal Caucasian women. Many studies indicate that there are important racial differences in skeletal health and fracture risk, an observation that makes the application of Caucasian data to all groups problematical. This study was undertaken to establish a BMD referent database in Chinese American women and to compare it with a Caucasian female database. It is expected that a race-specific database will be useful in the assessment of bone health for Chinese American women. METHODS: Healthy Chinese American women (n=359), ages 20-90, were recruited. Along with dual-energy X-ray absorptiometry (DXA) of the total hip and lumbar spine, demographic, medical, familial, nutritional, and behavioral data were obtained. The mean and standard deviation for BMD at each site was calculated for each 10-year age group and compared to mean BMD values for Caucasian women supplied as found in the Hologic DXA instrument. Osteoporosis diagnosis rates for this cohort, calculated with the Caucasian and newly established Chinese American BMD referent values, were compared with each other. RESULTS: Compared with Caucasian women, Chinese American women have significantly lower BMD at the lumbar spine, total hip, and femoral neck across a wide spectrum of age groups. As a consequence, more than one-half of Chinese American women>or=50 years of age, who would be characterized as osteoporotic using a Caucasian referent, would not be diagnosed as such if a Chinese American referent were utilized. CONCLUSION: Chinese American reference BMD values are significantly lower than those for Caucasian women. Future studies relating Chinese American BMD values to fracture risk are necessary in order to determine if ethnic database-derived T-scores would be more predictive of fracture risk and to develop meaningful diagnostic criteria for this population.
In 1999, Spain was the first country to officially start a National Program to try to identify cadavers and human remains which could not be identified by the use of traditional forensic approaches. This attempt is called "Phoenix Program". Two independent mitochondrial DNA (mtDNA) databases were generated, which can automatically compare and match identical or similar sequences. One is the Reference Database, with mtDNA sequences from maternal relatives of missing persons, who provide the samples (buccal swabs) voluntarily; the other is the Questioned Database, comprised of mtDNA data of unknown remains and cadavers. Although the first phase of the program (typing of all unidentified human remains) will probably not be completed until December 2003, positive identifications are being made in the interim. To date, more than 1,200 families have contacted Phoenix, and at least 280 reference samples and 48 questioned evidences have been analyzed. When mtDNA matches are found, another independent analysis is performed as a part of the quality control mechanism. Once a match is confirmed (so far in 6 cases), an attempt is made to analyze short tandem repeat (STR) loci. We call for international collaboration to make this effort valuable worldwide.
BACKGROUND: It is usually considered that the efficacy of electroconvulsive therapy is due to the induction of a seizure (20). Benzodiazepines are well known antiepileptics (11) and it is suggested that they should be withdrawn during electroconvulsive therapy (3). The purpose of our study was to determine the evidence that exists for this hypothesis in the literature. METHOD: We have reviewed the international literature on electroconvulsive therapy and benzodiazepines through the Medline and Pascal reference database, and performed a manual search of the major international journals. We have retained the references dealing with both benzodiazepine and electroconvulsive therapy. RESULTS: Up to June 1990, 16 references have been found (table I). Of these 16 references, 5 (6, 7, 12, 19, 25) are letters to the editor with no data reported. Six papers (1, 2, 8, 9, 14, 22) examine benzodiazepines as anesthetics and only focus on anesthetic variables, ignoring electroconvulsive therapy-treatment outcome. Only four studies (5, 17, 23, 24) actually examine the incidence of benzodiazepine use on electroconvulsive therapy. Of these, three studies (17, 23, 24) report the incidence of benzodiazepines used as tranquilizers or hypnotics on duration of the electroconvulsive therapy induced seizure. One is a retrospective study (24) showing a decrease in seizure duration due to benzodiazepine use. Of the two prospective studies one shows (23) no difference in seizure duration and the other one (17) a decrease. These studies, however, fail to actually examine how the antidepressive efficacy of electroconvulsive therapy is modified by benzodiazepine use. One recent study (5) measures the antidepressive efficacy of electro-convulsive therapy through the decrease of a validated depression scale. This is a randomized double-blind study examining a short acting benzodiazepine used as an anesthetic in lieu of methohexital. Electroconvulsive therapy efficacy does not appear impaired. CONCLUSION: From our review of the literature it appears that the supposed negative effect of benzodiazepines on the antidepressive action of electroconvulsive therapy has not been demonstrated. Further studies are necessary warranted.
The purpose of this study was to evaluate the clinical effectiveness of lifestyle interventions for preventing osteoporotic fractures in people at high risk. Data sources were electronic bibliographic databases, reference lists of systematic reviews, meta-analyses and included trials, registers of trials and conference databases. There was no language restriction. Study selection comprised randomized controlled trials (RCTs), with appropriate comparator groups and at least 8 weeks of follow-up, reporting a fracture endpoint. Two reviewers independently abstracted data on the population, interventions evaluated, trial quality and outcomes of interest: fractures at any site, spinal, hip and wrist fractures. Six RCTs, enrolling over 1,656 participants, met the inclusion criteria. Overall, trials were of uncertain quality. We categorized trials by type of intervention: exercise (n=3), multifactorial interventions (environmental modifications, exercise programs and review of medical conditions, medication and aids) (n=2) and exposure to sunlight (n=1), and used random effects meta-analyses to combine data within these categories. Exercise was associated with a non-significantly lower risk of spinal fractures (RR=0.52, 95% CI=0.17 to 1.60). Multifactorial interventions were associated with a lower risk of hip fracture, which was of borderline statistical significance (RR=0.37, 95% CI=0.13 to 1.03). Exposure to sunlight was associated with a non-significantly lower risk of hip fracture (RR=0.17, 95% CI=0.02 to 1.35). While withdrawals from treatment were poorly reported, there was no indication of adverse effects of treatment. Multifactorial interventions may reduce the risk of hip fractures when delivered by residential care staff and health visitors. More RCTs of higher quality, recording fractures at all sites susceptible to osteoporotic fractures, are necessary to evaluate exercise interventions, exposure to sunlight and the place of lifestyle alongside pharmacological interventions.
In high throughput sequence analysis, it is often necessary to combine the results of contemporary bioinformatics tools, because no individual tool alone computes all the requested information. ESTAnnotator is a tool for the high throughput annotation of expressed sequence tags (ESTs) by automatically running a collection of bioinformatics applications. In the first step, a quality check is performed and repeats, vector parts and low quality sequences are masked. Then successive steps of database searching and EST clustering are performed. Already known transcripts present within mRNA and genomic DNA reference databases are identified. Subsequently, tools for the clustering of anonymous ESTs, and for further database searches at the protein level, are applied. Finally, the outputs of each individual tool are gathered and the relevant results presented in a descriptive summary. ESTAnnotator was already successfully applied for the systematic identification and characterisation of novel human genes involved in cartilage/bone formation, growth, differentiation and homeostasis. ESTAnnotator is available at http://genome.dkfz-heidelberg.de, contact: genome@dkfz.de.
This paper aims to provide technical and practical advice about finding references using Current Contents on disk (Macintosh or PC) or via the Internet (FTP). Seven editions are published each week. They are all organized in the same way and have the same search engine. The Life Sciences edition, extensively used in medical research, is presented here in detail, as an example. This methodological note explains, in French, how to use this reference database. It is designed to be a practical guide for browsing and searching the database, and particularly for creating search profiles adapted to the needs of researchers.
The aim of this work was to provide an overview of the genetics of human ageing to gain novel insights about the mechanisms involved. By incorporating findings from model organisms to humans, such as mutations that either delay or accelerate ageing in mice, we constructed the gene networks previously related to ageing: namely, the network related to DNA metabolism and the network involving the GH/IGF-1 axis. Gathering data about the interacting partners of these proteins allowed us to suggest the involvement in ageing of a number of proteins through a "guilt-by-association" methodology. To organize our data, we developed the first curated database of genes related to human ageing: GenAge. With over 200 entries, GenAge may serve as a reference database of genes related to human ageing. Moreover, we rendered the first proteomic network map of human ageing, which suggests a relationship between the genetics of development and the genetics of ageing. Our work serves as a framework upon which a systems-biology understanding of ageing can be developed. GenAge is freely available for academic purposes at: http://genomics.senescence.info/genes/.
Bone mineral density (BMD) measurements using dual-energy X-ray absorptiometry (DXA) are widely used to diagnose osteoporosis and assess its severity. Previous studies show the necessity to establish reference data for bone mass measurements for each particular population. Such data are lacking for the Moroccan population. The aim of this study was to determine spine and femur BMD reference values for the Moroccan female population and to compare them with values from western and other Arab countries. A cross-sectional study of 569 Moroccan women, (randomly selected in the area of Rabat, the capital of Morocco, aged between 20 and 79 yr) was carried out to establish reference values of BMD. Measurements were taken at the lumbar spine and proximal femurs using DXA (Lunar Prodigy Vision, GE). The data were compared with published normative data taken by United States (U.S.), European, Kuwaiti, Lebanese, and Saudi women over 6 decades of age. The percentage of osteoporosis in postmenopausal women using our reference curve was compared to that observed when the other curves (US, European and Arab) implemented in the Lunar machine was used. Our results showed that the Moroccan women showed the expected decline in BMD at both sites with age after peaking at 20-29 years of age. Moroccan females have lower BMD at the spine than U.S., Europeans, and Kuwaitis (approximately 10-12% for patients older than 50 yr). The BMD values of the total femur in Moroccan females were close to western (European and American), and Kuwaitis, but higher than Lebanese and Saudis. Using our reference database, 37.9% of postmenopausal women had spine osteoporosis vs. 39.6% and 23.4% using US/European and Arabic Lunar reference values respectively. At the femurs, 6.7% had osteoporosis vs. 2.5% using the Arabic Lunar reference values. In conclusion, our study emphasizes the importance of using population-specific reference values for BMD measurements to avoid over or underdiagnosis of osteoporosis.