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PubMed1997

Preschool vision screening.

OBJECTIVES: To undertake a systematic review of the effectiveness of preschool vision screening. To provide evidence on which decisions about the future provision of this service can be made. To indicate areas for further research. STUDY SELECTION: The Centre for Reviews and Dissemination guidelines for systematic reviews were used. The research questions were formulated using the Wilson and Jungner criteria for evaluating screening programmes. They concerned prevalence, natural history, disability, treatment and screening in relation to three target conditions: amblyopia, refractive errors and squints which are not cosmetically obvious. Studies were considered for inclusion according to pre-determined criteria for the age group studied, the outcomes measured and the study design. The following types of study design were considered: cross-sectional studies of prevalence, cohort studies of natural history, any type of study (e.g., cross-sectional surveys, case-series, qualitative studies) of disability attributable to a target condition, controlled trials, observational studies and audits of screening programmes, and prospective controlled trials of treatment. DATA SOURCES: The following electronic databases were searched: Biological Abstracts, CINAHL, Embase, ERIC, IAC Health Periodicals, IAPV, Medline, Psychlit, Science Citation Index, System for Information on Grey Literature in Europe, DHSS-Data, Faculty of Public Health Medicine Database of Dissertations, Index of Scientific and Technical Proceedings, Dissertation Abstracts, Index of Theses, NHS Research Register, Public Health Information Sharing Database. A limited amount of handsearching was undertaken. Reference lists were scanned to identify other relevant studies, and requests for unpublished data were made to people working in the field. DATA EXTRACTION: Data was extracted by the first author and then checked by the second. DATA SYNTHESIS: Quantitative analysis was undertaken where possible. Qualitative analysis was performed where studies were too heterogeneous for the data to be combined, or for research questions that were not suitable for quantitative synthesis. RESEARCH FINDINGS: The electronic search yielded over 5000 references, and over 500 abstracts were downloaded from the databases for further scrutiny. A total of 85 studies were included in the main analysis. PREVALENCE: No studies were found with the primary aim of establishing the prevalence of visual defects in preschool children. Data from studies of screening programmes report a range of yields for all the target conditions combined of 2.4-6.1%. NATURAL HISTORY: No studies designed with the intention of documenting the natural history of the target conditions in children aged 3 or 4 years were found. Other studies that provide some natural history data suggest that mild degrees of amblyopia may resolve spontaneously. In the absence of information about natural history it is impossible to estimate the effect of treatment from studies without a control group that was not treated. DISABILITY: A total of 21 studies exploring disability in relation to the target conditions were included. The literature provides a reasonable basis for generating plausible hypotheses about the ways in which the target conditions might disable people, but is insufficient to draw any firm conclusions about their impact on quality of life. The research to date is not sufficient to determine appropriate outcomes for controlled trials of treatment. TREATMENT: Five randomised controlled trials of treatment and six prospective controlleld trials without randomisation were found. No studies compared treatment with no treatment. Most of the studies were methodologically flawed.(ABSTRACT TRUNCATED)

Child, Preschool↗
PubMed2001

Primary intrathoracic malignant effusion: a descriptive study.

BACKGROUND: Patients who present with malignant pleural/malignant effusion without a definite primary site are not well described in the medical literature. In the course of our clinical practice, we have observed certain traits that are peculiar to patients with such a presentation. We have applied the term primary intrathoracic malignant effusion (PIME) to describe this condition. STUDY OBJECTIVES: Patients must fulfill the following criteria before a diagnosis of PIME can be made: clinical presentation dominated by pleural/pericardial effusion; histologic proof of malignancy obtained from the pleura and/or pericardium; no definite primary site in the lungs or elsewhere from CT scan of the chest, chest radiograph, or physical and endoscopic examination; no history of malignancy; and no history of asbestos exposure. Exposure to environmental tobacco smoke (ETS) among the nonsmokers was examined in a case-control setting. METHODS: We conducted a retrospective search of our database of patients who were referred to the Department of Medical Oncology with a diagnosis of pleural/pericardial effusion from January 1993 to January 2000. RESULTS: Seventy-one of 200 patients from our database met the criteria. A significant majority of the patients were women (65%) and nonsmokers (72%). All patients had adenocarcinoma shown on biopsy. The majority of patients (63%) had disease localized to the intrathoracic serosal surfaces; the rest had distant metastases involving the lung (50%), bone (27%), liver (19%), brain (8%), and skin (4%). Six patients had two or more sites of distant metastases. There was a significant association with ETS exposure when compared to a control group comprised of patients with colonic cancer, matched for sex and age. The median survival was 10 months for patients with disease localized to the pleura/pericardium and 7 months for those with distant metastases. Thirty-eight patients (54%) received chemotherapy. All had platinum-based chemotherapy, except for three patients. The median survival for patients treated or not treated with chemotherapy was 12 months and 5 months, respectively. This difference in survival was statistically significant (p = 0.003). CONCLUSIONS: PIME should be viewed as a distinct entity. Its etiology remains largely unknown, although exposure to environmental tobacco smoke may play a part. Platinum-based chemotherapy may have a positive biological effect on this disease. More studies are required to elucidate the epidemiology, possible etiologic factors, and treatment options for this group of patients.

Adult↗
PubMed2004

Addressing the use of phylogenetics for identification of sequences in error in the SWGDAM mitochondrial DNA database.

The SWGDAM mtDNA database is a publicly available reference source that is used for estimating the rarity of an evidence mtDNA profile. Because of the current processes for generating population data, it is unlikely that population databases are error free. The majority of the errors are due to human error and are transcriptional in nature. Phylogenetic analysis of data sets can identify some potential errors, and coupled with a review of the sequence data or alignment sheets can be a very useful tool. Seven sequences with errors have been identified by phylogenetic analysis. In addition, two samples were inadvertently modified when placed in the SWGDAM database. The corrected sequences are provided so that users can modify appropriately the current iteration of the SWGDAM database. From a practical perspective, upper bound estimates of the percentage of matching profiles obtained from a database search containing an incorrect sequence and those of a database containing the corrected sequence are not substantially different. Community wide access and review has enabled identification of errors in the SWGDAM data set and will continue to do so. The result of public accessibility is that the quality of the SWGDAM forensic dataset is always improving.

Base Sequence↗
PubMedDate not supplied

Microcomputer database management for surgical residents.

Surgical residents must record procedures performed and may choose to keep files of photographic slides, bibliographic references, and a curriculum vitae. Four databases that store this information are produced with an inexpensive and easily obtained microcomputer software program. A surgical procedure database is modeled after the procedure list recommended by surgical boards. This list can be viewed while one enters data, thereby enabling production of accurate and complete records. In the second database, photographic slides are assigned sequence numbers and slide content is designated using both procedure codes and key words, allowing structured and personal recall of data. Data can be printed in many report formats, including that used by the boards of surgery for final submission of reports of residents' operations at the completion of residency. The bibliographic and CV databases contain highly segmented citation data. This structure enables manipulation of data to satisfy the sequence requirements of journals or institutions to which articles or CV are submitted. Database maintenance consumes a few minutes daily and requires a minimum of experience with computers. By providing ease of access to organized data, these databases enhance the potential for critical review of clinical experience by both residents and program directors.

General Surgery↗
PubMed1987

The use of a computerised database for the diagnosis of a rare neurological syndrome.

A database which runs on an office microcomputer is being developed for the diagnosis of genetically determined neurological disorders. At present about 1100 conditions with their clinical features and 3000 references are stored in the database. We discuss a family with 3 sibs affected by a unique neurological disorder and show how the database is used. The 3 sibs, 4, 5 and 10 years old, show the same clinical course characterized by congenital cataracts, microcephaly, hypotonia, mental retardation, pyramidal signs and choreoathetoid movements starting in early childhood. The parents are first cousins of Bangladeshi origin. This condition does not appear in published report and is not listed in the database. It can therefore be concluded that the sibs have a unique autosomal recessive disorder.

Athetosis↗
PubMed2006

Identification of medically important yeast species by sequence analysis of the internal transcribed spacer regions.

Infections caused by yeasts have increased in previous decades due primarily to the increasing population of immunocompromised patients. In addition, infections caused by less common species such as Pichia, Rhodotorula, Trichosporon, and Saccharomyces spp. have been widely reported. This study extensively evaluated the feasibility of sequence analysis of the rRNA gene internal transcribed spacer (ITS) regions for the identification of yeasts of clinical relevance. Both the ITS1 and ITS2 regions of 373 strains (86 species), including 299 reference strains and 74 clinical isolates, were amplified by PCR and sequenced. The sequences were compared to reference data available at the GenBank database by using BLAST (basic local alignment search tool) to determine if species identification was possible by ITS sequencing. Since the GenBank database currently lacks ITS sequence entries for some yeasts, the ITS sequences of type (or reference) strains of 15 species were submitted to GenBank to facilitate identification of these species. Strains producing discrepant identifications between the conventional methods and ITS sequence analysis were further analyzed by sequencing of the D1-D2 domain of the large-subunit rRNA gene for species clarification. The rates of correct identification by ITS1 and ITS2 sequence analysis were 96.8% (361/373) and 99.7% (372/373), respectively. Of the 373 strains tested, only 1 strain (Rhodotorula glutinis BCRC 20576) could not be identified by ITS2 sequence analysis. In conclusion, identification of medically important yeasts by ITS sequencing, especially using the ITS2 region, is reliable and can be used as an accurate alternative to conventional identification methods.

Ascomycota↗
PubMed2001

Dietary treatment for familial hypercholesterolaemia.

BACKGROUND: Familial hypercholesterolaemia is an inherited disorder characterised by a raised blood cholesterol, the presence of xanthomatosis and premature ischaemic heart disease. The aim of treatment is the reduction of blood LDL cholesterol concentrations in order to reduce the risk of ischaemic heart disease. Current treatment is based on a cholesterol lowering diet alone or in combination with drug therapy. Many of the drugs found to be effective in treating adults with this disease are not licensed for use in children, therefore diet is the main treatment of children with familial hypercholesterolaemia. In addition to the cholesterol-lowering diet, several other dietary interventions have been suggested and consensus has yet to be reached on the most appropriate dietary treatment for children and adults with familial hypercholesterolaemia. OBJECTIVES: To examine the evidence that in children and adults with familial hypercholesterolaemia, a cholesterol lowering diet is more effective at lowering cholesterol and reducing incidence of ischaemic heart disease than no intervention or than other dietary interventions. SEARCH STRATEGY: We searched the Cochrane Cystic Fibrosis and Genetic Disorders Trials Register, a specialist trials register which comprises references identified from comprehensive electronic database searches, handsearching relevant journals and handsearching abstract books of conference proceedings. Additional studies were identified from handsearching the Journal of Inherited Metabolic Disease (from inception, 1978 to 2000) and from the reference lists of identified studies. SELECTION CRITERIA: Randomised controlled trials (RCTs), both published and unpublished, where a cholesterol lowering diet in children and adults with familial hypercholesterolaemia has been compared to other forms of dietary treatment or to no dietary intervention. Trials which include patients with familial hypercholesterolaemia alongside patients with non-familial hypercholesterolaemia were only included if the group of familial patients was well defined and the results for these patients were available. DATA COLLECTION AND ANALYSIS: Two reviewers independently assessed the trial eligibility and methodological quality and one reviewer extracted the data, with independent verification of data extraction by a colleague. MAIN RESULTS: Only short term outcomes could be assessed in this review due to the length of the five eligible studies. Compliance to treatment, quality of life, mortality and evidence of ischaemic or atheromatous disease were not assessed in the studies identified. No differences were found between the cholesterol-lowering diet and all other diets for all of the short term outcomes assessed. REVIEWER'S CONCLUSIONS: No conclusions can be made about the effectiveness of the cholesterol-lowering diet, or any of the other dietary interventions suggested for familial hypercholesterolaemia, due to the lack of adequate data. A large, parallel, randomised controlled trial is needed to investigate the effectiveness of the cholesterol-lowering diet and other dietary interventions for FH. It is also possible that data from trials including subjects with both familial and non-familial hypercholesterolaemia could alter the results of future updates of this review and until further evidence is available current dietary treatment of FH should continue to be observed and monitored with care.

Adult↗
PubMed1996

Federated two-dimensional electrophoresis database: a simple means of publishing two-dimensional electrophoresis data.

While a two-dimensional electrophoresis (2-DE) database is a relatively old concept, in recent years it generated renewed interest within the 2-DE community due to two main factors: (i) The high reproducibility of the current 2-DE method allows 2-DE images to be exchanged and compared between laboratories. (ii) The recent development of faster and more powerful techniques for protein identification such as microsequencing, matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) and amino acid composition makes the production of reference protein maps and 2-DE databases cost- and time-effective. Additionally, the Internet network's current increase in popularity, combined with the rapid growth of Internet-connected laboratories, provides a straightforward means of publishing and sharing 2-DE data. While a small number of laboratories have already successfully published their data over the net, the increasing number of 2-DE database servers that are currently being set up will sooner or later require some kind of standardization. Unfortunately, standardization can be a long and cumbersome process inevitably leading to undesirable compromises. A federated database offers a simple and efficient way to publish and share 2-DE data without the need for standardization. Taking advantage of Internet protocols such as World Wide Web, they allow each laboratory to maintain their own database and to interconnect it with other similar databases through the use of active cross-references. This paper first presents guidelines for building a federated 2-DE database that may easily be followed by most laboratories. It then briefly reviews the state-of-the-art in networked 2-DE databases, and finally describes the SWISS-2DPAGE database which fully implements the concept of a federated 2-DE database.

Computer Communication Networks↗
PubMed1999

Update of the Human MitBASE database.

Human MitBASE is a database collecting human mtDNA variants. This database is part of a greater mitochondrial genome database (MitBASE) funded within the EU Biotech Program. The present paper reports the recent improvements in data structure, data quality and data quantity. As far as the database structure is concerned it is now fully designed and implemented. Based on the previously described structure some changes have been made to optimise both data input and data quality. Cross-references with other bio-databases (EMBL, OMIM, MEDLINE) have been implemented. Human MitBASE data can be queried with the MitBASE Simple Query System (http://www.ebi.ac.uk/htbin/Mitbase/mit base.pl) and with SRS at the EBI under the 'Mutation' section (http://srs.ebi.ac.uk/srs5/). At present the HumanMitBASE node contains approximately 5000 variants related to studies investigating population polymorphisms and pathologies.

Animals↗
PubMed2006

Does microalbuminuria predict illness severity in critically ill patients on the intensive care unit? A systematic review.

CONTEXT: Studies assessing the accuracy of microalbuminuria to predict illness severity on the intensive care unit have produced inconsistent results. OBJECTIVE: To determine the diagnostic accuracy of microalbuminuria to predict illness severity in critically ill patients on the intensive care unit. DATA SOURCE: MEDLINE (1951 to September 2004) and EMBASE (1980 to September 2004) electronic databases were searched for relevant studies. Reference lists of all abstracts were manually searched to identify studies not included in the electronic database. STUDY SELECTION: Studies that prospectively evaluated the accuracy of microalbuminuria to predict illness severity and/or mortality probability in adult patients on the intensive care unit were selected. DATA EXTRACTION: We included nine studies in the review. Data to evaluate methodological quality and results were abstracted. DATA SYNTHESIS: The methodological quality of a number of studies was poor. Significant heterogeneity in the design and conduct of the studies circumvented the data being subjected to meta-analysis. Studies also differed in the timing of the index test, in the methods of quantifying microalbuminuria, and in the cutoff values used. CONCLUSIONS: This descriptive analysis reveals that microalbuminuria may hold promise as a predictor of illness severity and mortality on the intensive care unit. However, future epidemiologic studies need to be conducted to determine the optimal timing as well as the threshold reference value for the urine albumin creatinine ratio in the adult intensive care unit population. Thereafter, multiple-center prospective epidemiologic studies must be conducted to confirm and validate the findings of these preliminary studies. Future studies should conform to the Standards for Reporting of Diagnostic Accuracy checklist in terms of study design, conduct, and reporting. Presently there is no evidence to warrant the use of this tool on the intensive care unit.

Albuminuria↗
PubMed1998

Compilation of DNA sequences of Escherichia coli K12: description of the interactive databases ECD and ECDC.

We have compiled the DNA sequence data for Escherichia coli K12 available from the GenBank and EMBL data libraries and independently from the literature. We provide the most definitive version of the ECD Escherichia coli database now exclusively via the World Wide Web System (http://susi.bio.uni-giessen.de/ecdc.html ). Our database encloses the completed genome sequence recently published by two competing groups and an assembled set of all elder sequences. The organisation of the database allows precise physical location of each individual gene or regulatory region, even taking into consideration discrepancies in nomenclature. The WWW program allows to the user to branch into the original EMBL and SWISS-PROT datafiles. A number of links to other WWW servers dealing with E. coli is provided. A FASTA and BLAST search may be performed online. Besides the WWW format a flat file version may be obtained via ftp. A number of discrepancies between the two systematic sequence determinations and/or the literature have not yet been resolved. However, our database may serve as a reference source for resolution and/or the assignment of strain difference.

Computer Communication Networks↗
PubMed2003

Development of a centralized inland marine hazardous materials response database.

The state of the practice for obtaining chemical reference at a typical hazardous materials transportation accident scene is to consult multiple printed references. This often leads to confusion. This paper describes the design and development of a centralized response database. This is accomplished by identifying the most commonly used emergency response databases for all modes of transportation, developing relationships between the data, and building intuitive interfaces that allow for rapid information retrieval. The tool is subsequently applied to a previous accident to demonstrate the value-added from its availability in a response scenario. By combining all datasets in one application, data redundancy, errors and lags between updates of the data sets can be reduced. The linkages between the database and supporting files enables the data to be easily updated. While the database is designed to aid response to marine transportation accidents, the tool could also be applied to other modes of transportation. Moreover, facility and vessel operators could benefit from having a comprehensive chemical source accessible in case of release or human contact with the material. Finally, the inclusion of commodity flow information enables decision makers to prepare for high risk commodities.

Accidents, Occupational↗
PubMed2005

How well are protein structures annotated in secondary databases?

We investigated to what extent Protein Data Bank (PDB) entries are annotated with second-party information based on existing cross-references between PDB and 15 other databases. We report 2 interesting findings. First, there is a clear "annotation gap" for structures less than 7 years old for secondary databases that are manually curated. Second, the examined databases overlap with each other quite well, dividing the PDB into 2 well-annotated thirds and one poorly annotated third. Both observations should be taken into account in any study depending on the selection of protein structures by their annotation.

Amino Acid Sequence↗
PubMed2000

The 1999 SWISS-2DPAGE database update.

SWISS-2DPAGE (http://www.expasy.ch/ch2d/ ) is an annotated two-dimensional polyacrylamide gel electro-phoresis (2-DE) database established in 1993. The current release contains 24 reference maps from human and mouse biological samples, as well as from Saccharomyces cerevisiae, Escherichia coli and Dictyostelium discoideum origin. These reference maps have now 2824 identified spots, corresponding to 614 separate protein entries in the database, in addition to virtual entries for each SWISS-PROT sequence or any user-entered amino acids sequence. Last year improvements in the SWISS-2DPAGE database are as follows: three new maps have been created and several others have been updated; cross-references to newly built federated 2-DE databases have been added; new functions to access the data have been provided through the ExPASy proteomics server.

Animals↗
PubMed2004

Development of a food database of nitrosamines, heterocyclic amines, and polycyclic aromatic hydrocarbons.

Some nitrosocompounds that are formed during food preservation, as well as polycyclic aromatic hydrocarbons (PAH) and heterocyclic amines (HA) formed during cooking, may have carcinogenic activity. An accurate assessment of dietary intake of such compounds is difficult, mainly because they are not naturally present in foods, and they are not included in standard food composition tables. Our objective was to develop a food composition database of nitrates, nitrites, nitrosamines, HA, and PAH. We conducted a literature search on the food content of these compounds using the Medline and EMBASE databases. We gathered the following information: 1) Food information: name, cooking methods, preservation methods, cooking doneness, temperature, and time; 2) compound information: type, quantity, value type, analytic method, and sampling methods; and 3) publication information: year, author, and country. We developed a table that includes 207 food items with information concerning the concentration of nitrites, nitrates, and nitrosamines, 297 food items with information about HA concentration and 313 food items with information about PAH. The database is based on 139 references from 23 different countries. It is arranged according to compounds and food groups to facilitate its practical use. The potential limitations are due to the quality of the information we could obtain through Medline and EMBASE databases. This database will allow investigators to quantify dietary exposure to several potential carcinogens, and to analyze their relation to the risk of cancer.

Carcinogens↗
PubMed2004

UniProt: the Universal Protein knowledgebase.

To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium. Our mission is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces. The central database will have two sections, corresponding to the familiar Swiss-Prot (fully manually curated entries) and TrEMBL (enriched with automated classification, annotation and extensive cross-references). For convenient sequence searches, UniProt also provides several non-redundant sequence databases. The UniProt NREF (UniRef) databases provide representative subsets of the knowledgebase suitable for efficient searching. The comprehensive UniProt Archive (UniParc) is updated daily from many public source databases. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt.

Animals↗
PubMed2002

Evaluation of referrals for genetic investigation of short stature in Hong Kong.

OBJECTIVE: To establish a profile of the causes of apparently unexplained SS in genetic referral center and evaluate the current referral system. METHODS: This was a retrospective database survey on patients who were referred our clinical genetic service from 1988 - 1998 primarily because of SS. We retrieved the study population from our computer database using "short stature"as a search handle and then studied the demographic, clinical and laboratory data from their medical records. RESULTS: Three hundred and fifty-three subjects were referred for genetic evaluation of SS in 1988 - 1998. The mean age of referred subjects was 11.5 years and the female to male ratio was 7.6. All referrals had undergone cytogenetic studies to exclude chromosomal abnormalities, 19% of girls with apparently unexplained short stature had Turner syndrome; at least 47.9% of the study population were normal variants and 25% of the referrals had inadequate information for classification. CONCLUSIONS: Genetic investigation is essential in the management of patients with SS, especially for girls suspected of having Turner syndrome, in which growth hormone treatment has shown to improve final height. We also highlight the inherited causes of short stature, which were often misdiagnosed as benign familial short stature, and discussed the drawbacks of the current referral system.

Child↗
PubMed2006

[Diabetics with normal coronary arteries: clinical features and prognosis].

BACKGROUND: Diabetic patients comprise a large proportion of patients referred for coronary angiography. Only a minority of these patients will be found to have normal coronary arteries. AIM: To characterize diabetic patients who have angiographically normal coronary arteries. METHODS: Case-control study based on a computerized database. RESULTS: Using our computerized database, 13,342 consecutive patients referred for coronary angiography were identified. Diabetes mellitus was diagnosed in 24% of cases. Angiographically normal coronary arteries were found in 151 (5%) and 1228 (12%) of diabetic and non-diabetic patients, respectively (p<0.01). Diabetic patients with angiographically normal coronary arteries were matched with 155 diabetic patients who were catheterized on the same day but were found to have coronary artery disease. The median follow-up period was 1,774 days. The age of the diabetic patients with normal coronary arteries and diabetic patients with coronary artery disease was 5710 and 6410 years old respectively (p<0.01). A total of 39% and 60% of diabetic patients with normal coronary arteries and with coronary artery disease respectively were males, (p<0.01). Dyslipidemia was diagnosed in 66 (43%) of the diabetic patients with normal coronary arteries and 87 (57%) of the diabetic patients with coronary artery disease (P<0.01). After controlling for age and sex, the finding of normal coronary arteries was associated with decreased mortality (OR: 0.47, 95% CI 0.23 to 0.95). CONCLUSIONS: In diabetic patients referred for angiography it is unusual to find angiogrtaphically normal arteries. These patients have a relatively benign prognosis, as opposed to diabetic patients with evident coronary disease.

Aged↗