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PubMed1998

[Selected aspects of computer-assisted literature management].

We want to report about our own experiences with a database manager. Bibliography database managers are used to manage information resources: specifically, to maintain a database to references and create bibliographies and reference lists for written works. A database manager allows to enter summary information (record) for articles, book sections, books, dissertations, conference proceedings, and so on. Other features that may be included in a database manager include the ability to import references from different sources, such as MEDLINE. The word processing components allow to generate reference list and bibliographies in a variety of different styles, generates a reference list from a word processor manuscript. The function and the use of the software package EndNote 2 for Windows are described. Its advantages in fulfilling different requirements for the citation style and the sort order of reference lists are emphasized.

Database Management Systems↗
PubMed2006

Systematic review: the use of mesalazine in inflammatory bowel disease.

BACKGROUND: Mesalazine is among the medications most commonly prescribed by gastroenterologists, having to a large extent superseded sulfasalazine (sulphasalazine). However, there are still a number of aspects regarding its use which provoke debate and controversy. AIM: To provide a systematic assessment of the evidence for the use of mesalazine in ulcerative colitis and Crohn's disease. METHODS: References were identified using PubMed database. Additional references were identified with related article searches. RESULTS: Mesalazine has a clear role in the maintenance of remission in ulcerative colitis and management of mild to moderately active disease, although the efficacy of topical preparations or combined topical and oral is clearly superior to oral alone. Evidence that increasing the dose of oral mesalazine improves efficacy is not clear-cut. The benefits of mesalazine in the management of acute Crohn's disease and the maintenance of remission are questionable and alternative treatments are usually more appropriate. Emerging evidence suggests that maintenance mesalazine reduces the risk of neoplastic progression in chronic ulcerative colitis. Compliance with therapy is thus important, as is an understanding of individuals most likely to default on this. CONCLUSION: Evidence for a beneficial effect of mesalazine is largely confined to the management of ulcerative colitis.

Acute Disease↗
PubMed2003

Vaccine safety surveillance using large linked databases: opportunities, hazards and proposed guidelines.

Combined administrative databases are referred to as 'large linked databases' because of their relatively large size and the need for linkage of different data sets that were created separately from each other. Such linked databases have become popular in vaccine safety surveillance. Whereas their use offers some unique opportunities, their increasingly widespread use can also lead to wrongful linkage of vaccines to adverse events. We review the opportunities and hazards of using large linked databases for vaccine safety surveillance and propose some guidelines to increase the reliability of the outcomes. We also offer our opinion on the future use of large linked databases for vaccine safety surveillance purposes.

Adverse Drug Reaction Reporting Systems↗
PubMed2003

A protocol for the update of references to scientific literature in biological databases.

Entries in biological databases are usually linked to scientific references. To generate those links and to keep them up-to-date, database maintainers have to continuously scan the scientific literature to select references that are relevant for each single database entry. The continuous growth of both the corpus of scientific literature and the size of biological databases makes this task very hard. We present a protocol intended to assist the updating of an existing set of literature (abstract) links from a single database entry with new references. It consists of taking the set of MEDLINE neighbour references of the existing linked abstracts and evaluating their relevance according to the existing set of abstracts. To test the applicability of the algorithm, we did a simple benchmark of the system using the references associated with the entries of a protein domain database. Human experts found the references that the algorithm scored highly were more relevant to the database entry than those scored lowly, suggesting that the algorithm was useful.

Abstracting and Indexing↗
PubMed2004

Characteristics of consultants who hold distinction awards in England and Wales: database analysis with particular reference to sex and ethnicity.

OBJECTIVE: To determine whether women, ethnic minorities, and particular specialties are discriminated against in the receipt of NHS distinction awards. DESIGN: Analysis of database of consultants eligible for distinction awards. SETTING: England and Wales, 2002. MAIN OUTCOME MEASURES: Holding of B, A, and Aplus distinction awards, analysed for all awards, irrespective of when made, and for awards made in the last five years studied. RESULTS: Women and doctors from ethnic minorities were substantially under-represented among award holders when no account was taken of potential confounding factors. Differences diminished after multivariate analysis, but some remained significant. For example, the adjusted odds ratio of women holding awards compared with men was 0.69 (95% confidence interval 0.59 to 0.82) for any award and 1.37 (0.86 to 2.20) for Aplus awards; the odds ratio for any award for non-white doctors trained abroad compared with white doctors trained in the United Kingdom was 0.45 (0.37 to 0.56). In the last five years studied the adjusted ratio of women to men was 0.94 (0.79 to 1.10) for B awards and 1.54 (0.85 to 2.83) for Aplus awards. The adjusted ratio for non-white British trained consultants was 0.86 (0.62 to 1.17) for B awards and 1.20 (0.37 to 3.87) for Aplus awards; for non-white consultants trained abroad it was 0.68 (0.54 to 0.85) for B awards and 0.69 (0.15 to 3.10) for Aplus awards; and for white consultants trained abroad it was 0.70 (0.54 to 0.91) for B awards and 0.90 (0.38 to 2.15) for Aplus awards. CONCLUSION: Historical under-representation in award holding by women and doctors from ethnic minorities was partly explained by time spent as a consultant. Recent awards showed no under-representation of women and no appreciable under-representation of ethnic minorities overall. However, doctors who trained abroad-both white and non-white-remained under-represented for B awards.

Awards and Prizes↗
PubMed2000

Inositol for respiratory distress syndrome in preterm infants.

BACKGROUND: Inositol is an essential nutrient required by human cells in culture for growth and survival. Inositol promotes maturation of several components of surfactant and may play a critical role in fetal and early neonatal life. OBJECTIVES: To assess the effectiveness/safety of supplementary inositol in preterm infants with RDS in reducing adverse neonatal outcomes. SEARCH STRATEGY: Medline, Embase, and Reference Update Databases were searched in August 1997 using key words: inositol and infant-newborn and random allocation or controlled trial or randomized trial (RCT). The reference lists of identified RCTs, personal files and Science Citation Index were searched. Unpublished additional information was obtained from the authors of one RCT published in abstract form. SELECTION CRITERIA: All randomized controlled trials of inositol supplementation to preterm infants with a control group that received a placebo or no intervention were included. Outcomes of interest were bronchopulmonary dysplasia (BPD), death, BPD or death, retinopathy of prematurity (ROP), intraventricular hemorrhage (IVH), necrotizing enterocolitis (NEC), and sepsis. DATA COLLECTION AND ANALYSIS: Data on neonatal outcomes were abstracted independently by the two researchers and any discrepancy was resolved through consensus. Revman was used for analysis of the data. MAIN RESULTS: Four reports of three RCTs were identified. One report was a duplicate publication. The outcome of death or bronchopulmonary dysplasia was reported in two trials, and was found to be significantly reduced (RR 0.56, 95% CI 0.42, 0.77; RD -0.215, 95% CI -0.323, -0.107). The outcome of death was reported in two trials and was found to be significantly reduced (RR 0.48, 95% CI 0.28, 0.80; RD -0.131, 95% CI -0.218, -0.043). Retinopathy of prematurity, stage 4 or needing therapy, was reported in two trials, and was found to be significantly reduced (RR 0.09, 95% CI 0.01, 0.67; RD -0.078, 95% CI -0.128, -0.027). Intraventricular hemorrhage, grade III-IV, was significantly decreased (RR 0.55, 95% CI 0.32, 0.95; RD -0.090, 95% CI -0.170, -0.010). Neither sepsis nor necrotizing enterocolitis outcomes were increased. When a secondary analysis was done excluding a study published in abstract form, the results differed only in that there was a significant reduction in retinopathy of prematurity, any stage (RR 0.53, 95% CI 0.29, 0.97; RD -0.082, 95% CI -0.159,-0.005). REVIEWER'S CONCLUSIONS: Inositol supplementation results in statistically significant and clinically important reductions in important short-term adverse neonatal outcomes. A multi-center RCT of appropriate size is justified to confirm these findings.

Dietary Supplements↗
PubMed2005

A nursing qualitative systematic review required MEDLINE and CINAHL for study identification.

OBJECTIVE: Analyze the number and the relevance of references retrieved from CINAHL, MEDLINE, and EMBASE to perform a nursing systematic review. STUDY DESIGN: A search strategy for the review topic was designed according to thesaurus terms. The study analyzes (1) references with abstract, (2) overlap between databases, (3) reference relevance, (4) relevance agreement between experts, and (5) reference accessibility. RESULTS: Bibliographic search retrieved 232 references: 16% (37) in CINAHL, 68% (157) in MEDLINE, and 16% (38) in EMBASE. Of these, 72% (164) were references retrieved with an abstract: 14% (23) in CINAHL, 70% (115) in MEDLINE, and 16% (26) in EMBASE. Overlap was observed in 2% (5) of the references. Relevance assessment reduced the number of references to 43 (19%): 12 (34.3%) in CINAHL, 31 (19.7%) in MEDLINE, and none in EMBASE (Z=-1.97; P=.048). Agreement between experts achieved a maximum Cohen's kappa of 0.76 (P < .005). References identified in CINAHL were the most difficult to obtain (chi(2)=3.9; df=1; P=.048). CONCLUSIONS: To perform a quality bibliographic search for a systematic review on nursing topics, CINAHL and MEDLINE are essential databases for consultation to maximize the accuracy of the search.

Bibliometrics↗
PubMed1996

[Derivation of latent reference intervals from routine laboratory database: its principle, validity and methodological implications for laboratory informatics].

A new method to derive reference from routine laboratory database intervals was developed. It depends on (1) availability of multiple screening tests results, (2) initial estimates for the reference intervals (RI) and (3) exclusion of data with multiple abnormalities in "related" test items. We designated those data which remained after exclusion as "latent reference values". RI was calculated from them parametrically employing a modified Box-Cox power transformation and maximal likelihood method. After RI were derived for all the items, they were used as a new set of RI estimates and the series of exclusion/calculation procedures were repeated for 7 times. The validity of the latent reference intervals (LRI) derived from routine biochemical screening test results were evaluated in three ways, by comparing them (1) with RIs determined conventionally from healthy individuals, and (2) with LRIs derived from qusi-normal individuals (blood donors), and (3) with LRIs obtained from a simulated healthy population which was generated as multivariate normal random values.

Adult↗
PubMed1999

The RESID Database of protein structure modifications.

Because the number of post-translational modifications requiring standardized annotation in the PIR-International Protein Sequence Database was large and steadily increasing, a database of protein structure modifications was constructed in 1993 to assist in producing appropriate feature annotations for covalent binding sites, modified sites and cross-links. In 1995 RESID was publicly released as a PIR-International text database distributed on CD-ROM and accessible through the ATLAS program. In 1998 it was made available on the PIR Web site at http://www-nbrf.georgetown.edu/pir/searchdb++ +.html . The RESID Database includes such information as: systematic and frequently observed alternate names; Chemical s Service registry numbers; atomic formulas and weights; enzyme activities; indicators forN-terminal, C-terminal or peptide chain cross-link modifications; keywords; and literature citations with database cross-references. The RESID Database can be used to predict atomic masses for peptides, and is being enhanced to provide molecular structures for graphical presentation on the PIR Web site using widely available molecular viewing programs.

Binding Sites↗
PubMed2004

Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment.

Several databases have been published to predict alternative splicing of mRNAs by analysing the exon linkage relationship by alignment of expressed sequence tags (ESTs) to the genome sequence; however, little effort has been made to investigate the relationship between cancers and alternative splicing. We developed a program, Alternative Splicing Assembler (ASA), to look for splicing variants of human gene transcripts by genome-wide ESTs alignment. Using ASA, we constructed the biosino alternative splicing database (BASD), which predicted splicing variants for reference sequences from the reference sequence database (RefSeq) and presented them in both graph and text formats. EST clusters that differ from the reference sequences in at least one splicing site were counted as splicing variants. Of 4322 genes screened, 3490 (81%) were observed with at least one alternative splicing variants. To discover the variants associated with cancers, tissue sources of EST sequences were extracted from the UniLib database and ESTs from the same tissue type were counted. These were regarded as the indicators for gene expression level. Using Fisher's exact test, alternative splicing variants, of which EST counts were significantly different between cancer tissues and their counterpart normal tissues, were identified. It was predicted that 2149 variants, or 383 variants after Bonferroni correction, of 26 812 variants were likely tumor-associated. By reverse transcription-PCR, 11 of 13 novel alternative splicing variants and eight of nine variants' tissue specificity were confirmed in hepatocellular carcinoma and in lung cancer. The possible involvement of alternative splicing in cancer is discussed.

Alternative Splicing↗
PubMed2000

Structure and presentation of a World Wide Web database of CSF virus isolates held at the EU reference laboratory.

A computerized database was generated with the epidemiological data of more than 600 CSF virus strains and isolates kept in the EU Reference Laboratory for Classical Swine Fever in Hanover. In addition, as sequence data from defined regions of the genome are increasingly being used for genetic typing of new isolates and are thus being published, it was decided to integrate them into the database. In order to make the epidemiological and the sequence data available to other laboratories through the World Wide Web, a searchable web interface was programmed, which can be accessed using an Internet browser like Netscape or Internet Explorer. The possibility to exchange data via the web has the potential to increase our knowledge concerning genetic and epidemiological links between outbreaks worldwide.

Animals↗
PubMed2001

[Reference manager EndNote 4. Further development and new functions].

Bibliography database managers are used to manage information resources: specifically, to maintain a database of references and create bibliographies and reference lists for written works. It should offer tools that let you find and retrieve references quickly, and it should be able to produce the bibliography in the format required for a particular publication. There are many computer programs, but very few stands out as truly useful, time saving, and work enhancing. One of them is EndNote. The reference manager EndNote 4 was recently released in Germany and, as long-time fans of this excellent program, we upgraded from the previous version. The use of the software package EndNote 4 for Windows is described, and we want to report about our own experiences with the new version of this database manager. The main reason for getting EndNote 4 is its clearly improved functions and features: for instance a new library window, a better search functions, an automatic updates and completion of term lists and an improved identification of duplicate references. Altogether EndNote 4 provides also an excellent combination of features and ease of use.

Database Management Systems↗
PubMed2001

Special report: NIST workshop on reference data for the properties of biomaterials.

A workshop on Reference Data for Biomaterials was held at the National Institute of Standards and Technology (NIST) on July 27, 2000. The primary purpose of the workshop was to determine whether needs existed for the establishment of reference data (RD) databases on the properties of biomaterials. Special attention was given to critiqued RD such as those traditionally found in databases that are established within the NIST Standard Reference Data Program. Critiqued data are data that have been critically evaluated for issues dealing with components of uncertainty, experimental design (details, descriptions, and appropriateness), measurement methods (appropriateness), conclusions drawn from the data, and so forth. Among the workshop's 65 registrants were representatives from industry, the National Institutes of Health (NIH), the Food and Drug Administration (FDA), and academia. These joined with NIST staff to address reference biomaterial property database needs within five categories: orthopedic, cardiovascular, ophthalmologic, tissue-engineered, and dental biomaterials. A general session on other issues focused specifically on database accesses (portals), contents, and maintenance. While the workshop's intended focus was on critiqued RD, it was suggested that closely related issues be considered as well. In this way, a more comprehensive assessment of opportunities for the cooperation of NIST with the biomaterials community might be developed. As a result, the needs for noncritiqued data and for reference materials (RMs), useful for developing data, also became a part of the focus of the workshop. Hence, this article presents the results from the breakout sessions of the workshop according to two categories: reference data and databases, and reference materials. In the following summary, the workshop is presented in the following order: An introduction to databases, resource presentations, action items identified in breakout sessions, assessment of resources (personnel and monetary) needed to work on action items, and portals for databases. Except for the individual concurrent breakout sessions themselves, all other sessions of the workshop were participated in fully by those in attendance.

Animals↗
PubMed2004

Nordic Reference Interval Project Bio-bank and Database (NOBIDA): a source for future estimation and retrospective evaluation of reference intervals.

In the Nordic Reference Interval Project 2000 (NORIP) serum, Li-heparin plasma and EDTA buffy coat were collected at 102 laboratories in 5 Nordic countries from healthy individuals aged 18 years or more and evenly distributed for laboratory, gender and age. Multiple aliquots of these samples from each of about 3000 persons are now stored at the Nordic Reference Interval Project Bio-bank and Database (NOBIDA) at a temperature of below -80 degrees C. The commutable NFKK Reference Serum X with certified values traceable to reference methods and measured in NORIP in the same series as the samples is also available from NOBIDA. Data describing the person and the sample conditions are stored together with analytical results and data describing the measurement systems. The bio-bank along with material and data is administered by the NOBIDA committee on behalf of the NFKK (Scandinavian Society of Clinical Chemistry) to be used by Nordic laboratories for any purpose beneficial to the development of clinical biochemistry in general and particularly for creating reference intervals for other biochemical properties than those established by NORIP. Furthermore, research on the already stored information alone is encouraged. Thus colleagues are now welcome to use this extensive material for research and development in clinical biochemistry.

Adolescent↗
PubMed2002

Radiographic changes in the lumbar intervertebral discs and lumbar vertebrae with age.

STUDY DESIGN: Plain lateral radiographs of the lumbar spines of 607 women (age range 20-87 years) and 633 men (age range 20-92 years) were studied. OBJECTIVE: To study the radiographic changes in the lumbar intervertebral discs and lumbar vertebrae with age. To compile a database of reference values for the age-dependent height of lumbar discs and concavity index of lumbar vertebral bodies as well as prevalence of vertebral osteophytes by age and sex. SUMMARY OF BACKGROUND DATA: There is a general agreement that changes induced by aging lead to alterations in the thickness of the disc, but there are differences in the accounts of the effect of aging on the thickness of the lumbar discs. Published methods to measure disc height yield, except for some exceptional cases, inaccurate results. Reference values of disc height and concavity index of lumbar vertebral bodies, suitable for quantitative comparison with a given disc and lumbar vertebral body, have yet to be established. METHODS: Using a new protocol with a precision of 3.9%, the anulus heights of lumbar discs were measured from sets of lateral radiographic views of 607 women and 633 men. The measurement of concavity index of vertebrae was established for each vertebral body by dividing the central vertebral height by the anterior vertebral height. RESULTS: The heights of lumbar discs T12-L1, L1-L2, L2-L3, L3-L4, L4-L5, and L5-S1 of men and women within the age 20-69 years increased with increasing age (4.6-6.9% in men and 4.7-8.4% in women). The concavity index of vertebrae T12, L1, L2, L3, L4, and L5 of men within age 20-87 years and of women within age 20-92 years decreased linearly with increasing age (0.9-1.5% in men and 1.6-3.2% in women). In other words, the vertebral body endplates became more concave with age. The prevalence of osteophytes was greater in men than in women in lumbar spine and increased with age. CONCLUSIONS: Using the new procedure and the database of reference values, it is possible to measure the height of lumbar discs and concavity of vertebrae objectively and precisely and to compare the results quantitatively with reference values.

Adult↗
PubMed2005

The Universal Protein Resource (UniProt).

The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the Swiss-Prot, TrEMBL and PIR protein database activities, the UniProt consortium produces three layers of protein sequence databases: the UniProt Archive (UniParc), the UniProt Knowledgebase (UniProt) and the UniProt Reference (UniRef) databases. The UniProt Knowledgebase is a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase with extensive cross-references. This centrepiece consists of two sections: UniProt/Swiss-Prot, with fully, manually curated entries; and UniProt/TrEMBL, enriched with automated classification and annotation. During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; we introduced a new comment line topic: TOXIC DOSE to store information on the acute toxicity of a toxin; the UniProt keyword list got augmented by additional keywords; we improved the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications. Furthermore, we introduced a new documentation file of the strains and their synonyms. Many new database cross-references were introduced and we started to make use of Digital Object Identifiers. We also achieved in collaboration with the Macromolecular Structure Database group at EBI an improved integration with structural databases by residue level mapping of sequences from the Protein Data Bank entries onto corresponding UniProt entries. For convenient sequence searches we provide the UniRef non-redundant sequence databases. The comprehensive UniParc database stores the complete body of publicly available protein sequence data. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). New releases are published every two weeks.

Amino Acid Sequence↗
PubMed2002

Denaturing gradient gel electrophoretic multilocus sequence typing of Staphylococcus aureus isolates.

To obviate the need for multilocus sequencing, a method using denaturing gradient gel electrophoresis (DGGE) was developed for the multilocus sequence typing (MLST) of Staphylococcus aureus isolates. Sequence types (STs) were obtained on the basis of sequences of polymerase chain reaction (PCR) products from seven housekeeping genes and compared to the reference MLST database. The melt curves, sequences and DGGE profiles were compared for 100 STs (i) to determine PCR conditions with 40-mer GC-clamps attached to the forward and reverse primers; (ii) to choose single restriction enzyme sites for digestion of PCR products into two fragments each with a GC-clamp attached and (iii) to optimize DGGE conditions. When the DGGE types (DT) were analyzed, the majority of DTs (76/100) were accurately classified into one ST (95% of nucleotide changes were detected), 10 DTs were classified into one of two STs corresponding to a single nucleotide ambiguity and 14 DTs were classified into 3 or 4 STs corresponding to 4 or 5 nucleotide ambiguities. A combination of STs and DTs were used to obtain septuplet sets of STs (7-ST) for 25 S. aureus isolates. When compared to the reference MLST database, one methicillin-resistant S. aureus (MRSA) isolate had the same genotype as the first MRSA clone. The DGGE-MLST method can be used as a rapid, accurate and 20-fold less expensive method than DNA sequencing for the detection of all sequence types. This combined laboratory and in silico approach could have wide applicability not only to MLST methods for other bacteria but to the screening of multilocus nucleotide differences deposited in other mutation databases.

Alleles↗
PubMed2003

Reference values of F wave parameters in healthy subjects.

OBJECTIVE AND METHODS: A large reference value database for F wave parameters was constructed with data from 121 to 196 healthy subjects; the age range of the subjects was 14-95 years. We studied the following parameters: minimum F wave latency (FMINLAT), mean F wave latency (FMEANLAT), maximum F wave latency (FMAXLAT), number of F waves/20 stimuli (FNUMBER) and F wave dispersion (FDISP=FMAXLAT-FMINLAT). The median, ulnar, peroneal and tibial nerves were studied. RESULTS: Height explains almost half of the FMINLAT variability. The F wave latency increases with height in the arms by 0.2 ms/cm and in legs 0.4 ms/cm. The effect of age on F wave latency in the arms is relatively small, only 0.03 ms/year; and in the legs age increases the FMINLAT by 0.1 ms/year. Gender does not affect FMINLAT in a systematic way. The peroneal nerve has slightly longer FMINLAT than the tibial nerve, while the FNUMBER is higher in the tibial nerve than the peroneal nerve. The differences between the ulnar and median nerve are slight. There is a very high correlation between all 3 latency parameters (FMINLAT, FMAXLAT and FMEANLAT), but no correlation between FDISP and FNUMBER and the other parameters. Side to side comparisons reveals no significant differences in any of the parameters except for the median nerve FMINLAT and FMEANLAT, which is 0.2 ms longer on the right than left. If side difference of more than 2 standard deviation is taken as the upper limit for normal, the side difference in arms is 1.4 ms and in legs 3 ms. In repeated studies the interexaminer variability is small; the correlation coefficient between the different F parameters is high (P>0.6 in arms and P>0.7 in legs). In the arms the upper limit for a significant difference of FMINLAT on repeated studies in the median nerve is 1.0 and 1.7 ms for the ulnar nerve. In the legs, FMINLAT for the peroneal nerve is 2.6 ms and for the tibial nerve is 2.1 ms. CONCLUSIONS: This large reference value database can be used not only to evaluate single measurements in relation with height and age, but also to compare right and left side and changes over time at repeated studies.

Adult↗