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PubMed1994

Biological Macromolecule Crystallization Database, Version 3.0: new features, data and the NASA archive for protein crystal growth data.

Version 3.0 of the NIST/NASA/CARB Biological Macromolecule Crystallization Database (BMCD) includes crystal and crystallization data on all forms of biological macromolecules which have produced crystals suitable for X-ray diffraction studies. The data include summary information on each of the macromolecules, crystal data, crystallization conditions and comments about the crystallization procedure if it varies from the traditional methods employed for crystal growth. The database-management software maintains continuity with previous versions providing similar search procedures and displays. Version 3.0 of the BMCD includes protocols and results of crystallization experiments undertaken in space. These new data are comprised of both the NASA Protein Crystal Growth Archive, which includes information on all NASA-sponsored protein crystal growth experiments, and data describing other internationally sponsored microgravity macromolecule crystallization studies. The entries for the space growth crystallization experiments contain the crystallization protocols, apparatus descriptions, flight summary data, indication of success or failure of the experiments, references, etc. Other new features of the BMCD include the addition of crystallization procedures for small peptides and cross references to other structural biology databases.

Journal Article↗
PubMed2002

ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data.

With the recent quick expansion of DNA and protein sequence databases, intensive efforts are underway to interpret the linear genetic information of DNA in terms of function, structure, and control of biological processes. The systematic identification and quantification of expressed proteins has proven particularly powerful in this regard. Large-scale protein identification is usually achieved by automated liquid chromatography-tandem mass spectrometry of complex peptide mixtures and sequence database searching of the resulting spectra [Aebersold and Goodlett, Chem. Rev. 2001, 101, 269-295]. As generating large numbers of sequence-specific mass spectra (collision-induced dissociation/CID) spectra has become a routine operation, research has shifted from the generation of sequence database search results to their validation. Here we describe in detail a novel probabilistic model and score function that ranks the quality of the match between tandem mass spectral data and a peptide sequence in a database. We document the performance of the algorithm on a reference data set and in comparison with another sequence database search tool. The software is publicly available for use and evaluation at http://www.systemsbiology.org/research/software/proteomics/ProbID.

Algorithms↗
PubMed2003

Analysis of cigarette smoking habits of cancer patients referred to the Northeastern Ontario Regional Cancer Centre.

PURPOSE: To review cigarette smoking among patients referred to the Northeastern Ontario Regional Cancer Centre (NEORCC). METHODS: Database analysis of the smoking history information for patients referred to the NEORCC from 1991-1999 was performed. RESULTS: Data was available for 15,850 patients and 72.7% reported being either current or previous smokers. Approximately 24.5% of patients were still smoking and 7.8% had quit within the last year. Smoking rates and total consumption were highest among those patients with cancers arising in the lung, bladder, esophagus and head & neck regions. The percentage of patients reporting a history of smoking remained consistently high over the time period studied. CONCLUSIONS: Cigarette smoking rates are high among NEORCC patients and strategies to improve the situation are required.

Adolescent↗
PubMed1997

Liaison psychiatry in an HIV/AIDS unit.

OBJECTIVE: To provide an overview of the work of a liaison psychiatry service to an HIV/AIDS inpatient unit, and particularly to examine the identification of mood and related disorders by referring doctors. METHOD: The MICRO-CARES prospective clinical database system was used to obtain data on all patients referred to the HIV/AIDS consultation-liaison psychiatry service in an infectious diseases hospital in Melbourne. RESULTS: Three hundred and ninety-two inpatient referrals were made in the 2 years from 1993-1995: a referral rate of 16.7%. The most frequent reasons for referral were evaluation of coping problems (42%), assessment of possible depression (31%), and assessment of psychotropic medication (24.5%). The most common psychiatric diagnoses were mood disorders (36.5%), psychoactive substance use disorders (22.7%) and organic mental disorders (18.1%). Overall concordance of recognition of depression by the referring doctor and diagnosis of depression by the consultant psychiatrist was 79%; 20% false positive rate, 23% false negative rate. CONCLUSIONS: Psychiatric comorbidity is common in patients with HIV/AIDS. Reasons for referral vary from those seen in other inpatient settings. Previously noted problems such as the misdiagnosis of psychiatric disorder and the mislabelling of the syndrome recognised by psychiatrists as depression were noted here.

Acquired Immunodeficiency Syndrome↗
PubMed2000

Spironolactone versus placebo or in combination with steroids for hirsutism and/or acne.

BACKGROUND: Hirsutism is the presence of excessive hair growth in women and is an important cosmetic condition often resulting in severe distress. Hirsutism is most often caused by increased production of male sex hormones also known as androgens. It is also affected by increased sensitivity to androgens in the hair follicles, and the secretory glands around the hair follicles, called sebaceous glands. Spironolactone is an antiandrogen and aldosterone antagonist used to treat hirsutism. Since 1978, many studies have been conducted to determine its effectiveness. OBJECTIVES: The objective of this review was to investigate the effectiveness of spironolactone and/or in combination with steroids (oral contraceptive pill included) in reducing excess hair growth and/or acne in women. SEARCH STRATEGY: All publications of randomised controlled trials of spironolactone versus placebo and/or in combination with steroids (oral contraceptive pill included) were identified. Search strategy was developed by the Menstrual Disorder Group. All accessable electronic databases were searched. In addition, all reference lists of relevant trials were searched and drug companies contacted for details of unpublished trials. SELECTION CRITERIA: All randomised controlled comparisons of spironolactone versus: placebo steroids (oral contraceptive pill included)) spironolactone of varying dosages or spironolactone and steroids versus steroids alone when used to reduce hair growth and acne in women. DATA COLLECTION AND ANALYSIS: Four trials were included in the review, seven trials were excluded. Two other trials are awaiting assessment. All included trials were small (no more than 31 participants) randomised and controlled. Only one trial studied acne as an outcome, the remaining three were concerned with hirsutism. One trial investigated spironolactone versus placebo; one trial was a dosage studies of spironolactone; one trial compared spironolactone with spironolactone in combination with dexamethasone; the remaining trial used topical spironolactone for the treatment of acne. Major outcome measures include the following: - subjective observations - Ferriman and Gallwey hair scores - hormonal and biochemical parameters - side effects - sebum production measurement MAIN RESULTS: All sample populations were small and confidence intervals were wide. There was no significant difference between treatments for any of the observed outcomes. REVIEWER'S CONCLUSIONS: The effectiveness of treatment for either acne vulgaris or hirsutism cannot be determined due to the small sample populations involved in the trials. Its value in clinical practice is difficult to assess from currently available research.

Acne Vulgaris↗
PubMed2001

Specialist epilepsy nurses for treating epilepsy.

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 the perceived deficiencies and suggestions to improve 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 is to overview the evidence from controlled trials investigating the effectiveness of specialist epilepsy nurses compared to routine care. SEARCH STRATEGY: The following databases were searched: The Cochrane Controlled Trials Register (The Cochrane Library, Issue 4, 1999), MEDLINE, GEARS, BIDS (EMBASE=Excepta Medica), 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. SELECTION CRITERIA: All randomized controlled and quasi-randomized trials which considered specialist epilepsy nurse interventions with standard or alternative care were included in this review. DATA COLLECTION AND ANALYSIS: Two reviewers independently selected trials for inclusion and extracted the relevant data. The following outcomes were assessed: (a) seizure frequency (b) appropriateness of medication prescribed (c) social or psychological functioning scores (d) knowledge about epilepsy scores (e) objective measures of general health status/quality of life (f) patients' reports of information received (g) number of days spent on sick leave/missing school and employment status (h) costs of care (i) adverse effects. MAIN RESULTS: Three trials were included, two based in general practice and one in a neurology centre. The population of patients differed between trials, for example one study excluded patients with learning disabilities, and one only recruited patients with a new diagnosis. In view of this heterogeneity we decided not to pool results in a meta-analysis. As yet, there is no convincing evidence that specialist epilepsy nurses improve outcomes for people with epilepsy overall. Important outcomes (e.g. seizure frequency, psychosocial functioning, knowledge of epilepsy, general health status, work days lost, depression and anxiety scores) show no significant improvement. There is some evidence that those patients who have not had an epileptic seizure in the last six months are less at risk for depression. There is also evidence that newly diagnosed patients whose knowledge about epilepsy is poor may improve their epilepsy knowledge scores after nurse intervention. REVIEWER'S CONCLUSIONS: It is clearly plausible that specialist epilepsy nurses could improve quality in epilepsy care. However, there is as yet little evidence to support this assumption as the present research base is small. Further research is needed to investigate the effectiveness of specialist epilepsy nurses before such recommendations can be made.

Epilepsy↗
PubMed1996

Consultation-liaison psychiatry in an obstetric service.

OBJECTIVE: The aim of this paper is to provide an overview of the work of a consultation-liaison (C-L) psychiatry service to an obstetric inpatient unit in a university affiliated teaching hospital, with the aid of a comprehensive clinical database. METHOD: The MICRO-CARES clinical database system was used for prospective recording of data on all obstetric inpatients referred to the C-L psychiatry service and the hospital clinical database was used to compare referred inpatients with all obstetric inpatients. RESULTS: Ninety patients were referred in 3 years, a referral rate of 1.2% of obstetric admissions. There was no bias in referral on age, but there were significantly more unmarried patients in the referred group (p < 0.001). Referred patients had a significantly prolonged length of stay: a mean of 9 days for referred patients, with 6 days for all obstetric patients (p < 0.001). The most frequent reasons for referral were: coping problems, depression, anxiety/fear and past history of major psychiatric illness. The most common DMS-III-R psychiatric diagnoses were: Personality Disorders (19%), Mood Disorders (17%), Schizophrenic Disorders (15%) and Adjustment Disorders (13%). At least one confirmed diagnosis was made in 77% of patients, but 42% of diagnoses remained differential. There were significantly more patients with diseases of the nervous system, endocrine and circulatory disorders in the referred group (p < 0.001). Recommendations of psychosocial interventions predominated over psychopharmacological interventions, and concordance with these was 97% and 98%, respectively. Issues in the relationship of obstetrics and psychiatric C-L services are discussed and future directions indicated. CONCLUSIONS: The referral rate was low compared with other specialty units. This is probably due to factors inherent in obstetric practice. A wide spectrum of psychiatric disorders was referred, including a higher than expected number of women with postpartum psychotic disorders, the majority of whom were managed successfully in the obstetric ward. There is a need for increased liaison with obstetric and community services and for collaborative research, with a particular emphasis on the prevention of psychiatric morbidity associated with pregnancy.

Adaptation, Psychological↗
PubMed2006

MitoP2: the mitochondrial proteome database--now including mouse data.

The MitoP2 database (http://www.mitop.de) integrates information on mitochondrial proteins, their molecular functions and associated diseases. The central database features are manually annotated reference proteins localized or functionally associated with mitochondria supplied for yeast, human and mouse. MitoP2 enables (i) the identification of putative orthologous proteins between these species to study evolutionarily conserved functions and pathways; (ii) the integration of data from systematic genome-wide studies such as proteomics and deletion phenotype screening; (iii) the prediction of novel mitochondrial proteins using data integration and the assignment of evidence scores; and (iv) systematic searches that aim to find the genes that underlie common and rare mitochondrial diseases. The data and analysis files are referenced to data sources in PubMed and other online databases and can be easily downloaded. MitoP2 users can explore the relationship between mitochondrial dysfunctions and disease and utilize this information to conduct systems biology approaches on mitochondria.

Animals↗
PubMed1992

Comparison of six microcomputer dietary analysis systems with the USDA Nutrient Data Base for Standard Reference.

We compared the general operating features and nutrient databases of six microcomputer dietary analysis systems. A 3-day food record with 73 food items was entered into each program; nutrient averages were compared with the US Department of Agriculture Nutrient Data Base for Standard Reference (USDA NDB), full version, release 9, for microcomputers. The six programs were found to vary widely in cost, number of foods and nutrients in the database, use of non-USDA data and imputation of data for missing values, number of print/export options, time to analyze the 3-day food record, and overall ease of use. Although all of the microcomputer dietary analysis systems were within 7% of the USDA NDB for energy, protein, total fat, and total carbohydrates, the proportion of other nutrients varying more than 15% from the USDA NDB varied considerably between programs. Variance among programs for 3-day food record nutrient values occurred because of differences in the number of food items included in the database (leading to varying degrees of substitution), the recency of the nutrient data (whether or not the most recent USDA releases had been incorporated), and the number of missing values (the degree to which non-USDA sources or estimated calculations were used to fill in the blanks from the USDA standard). Our results demonstrate that it is important for each dietitian to carefully choose a microcomputer dietary analysis system that is suitable to specific and predetermined needs.

Databases, Factual↗
PubMed2005

Do we need a Unique Scientist ID for publications in biomedicine?

BACKGROUND: The PubMed database contains nearly 15 million references from more than 4,800 biomedical journals. In general, authors of scientific articles are addressed by their last name and forename initial. DISCUSSION: In general, names can be too common and not unique enough to be search criteria. Today, Ph.D. students, other researchers and women publish scientific work. A person may not only have one name but several names and publish under each name. A Unique Scientist ID could help to address people in peer-to-peer (P2P) networks. As a starting point, perhaps PubMed could generate and manage such a scientist ID. SUMMARY: A Unique Scientist ID would improve knowledge management in science. Unfortunately in some of the publications, and then within the online databases, only one letter abbreviates the author's forename. A common name with only one initial could retrieve pertinent citations, but include many false drops (retrieval matching searched criteria but indisputably irrelevant).

Journal Article↗
PubMed2002

AGEID: a database of aging genes and interventions.

The aging genes/interventions database (AGEID) is a database of experimental results related to aging. AGEID is available as part of the science of aging knowledge environment on the World Wide Web at http://sageke.sciencemag.org/cgi/genesdb. The goal of AGEID is to catalog, in one location, every published experiment where life span has been measured in any organism. AGEID also includes information on genes that influence the incidence of age-associated disorders such as Alzheimer's disease and Parkinson's disease. AGEID gene/intervention reports are formatted pages containing the organism and strain background in which the particular experiment was performed, the type of genetic or environmental perturbation, the effect on life span, a description of the gene function and its role in longevity, protein homologs, and references. The use of this database by researchers who study aging should facilitate easy comparison of the genes and interventions that affect life span in different organisms.

Aging↗
PubMed2003

Is it clinically useful to repeat a pap smear at colposcopy?

OBJECTIVE: To assess the role of repeating a Pap smear at the time of colposcopy performed within 6 months of a referent Pap smear. MATERIALS AND METHODS: A clinical database was queried to identify colposcopies performed within 6 months of a referent abnormal squamous Pap smear at which time a repeat Pap smear was obtained. All Pap smears and cervical biopsy specimens were interpreted at an affiliated hospital laboratory. Referent Pap smears, repeat Pap smears, colposcopic cervical biopsy results, patient age and ethnicity, and the interval since the referent Pap smear were tabulated. A hierarchy of Pap smear results was defined a priori to characterize the relative differences between the referent and repeat Pap smears. Results of repeat smears and cervical biopsies were contrasted with the referent Pap smears. An assessment was made of the clinical usefulness of the repeat Pap smear. RESULTS: Four hundred ninety-eight patients contributed 536 colposcopies with repeat Pap smears within 6 months of the referent smear. Pap smears obtained at colposcopy predominantly were either of lower severity (52.2%) or unchanged (42%). Management of 8 of 498 patients (1.6%) was influenced by the results of the repeat Pap smear. The outcomes for six recommendations for a loop electrosurgical excision procedure included three cases of diagnoses of potentially reversible conditions. CONCLUSIONS: The evidence for the clinical usefulness of repeating a Pap smear at colposcopy for a squamous cytologic abnormality under the defined study parameters is noncompelling. Continued surveillance is a critical component of management.

Journal Article↗
PubMedDate not supplied

Challenges of high throughput screening against cell surface receptors.

Excessive or inappropriate activation of cell surface receptors can mediate the development of disease. Receptors, therefore, are a focus for drug discovery activities. Empirical screening is important in the search for novel compounds acting as receptors. Technical developments and the application of molecular biology have facilitated access to receptors of interest and have provided efficient screening methods capable of very high throughput. Reliability in high throughput screening requires the use of appropriate methodology, good screen design and effective validation and quality control processes. Validation should aim to establish that the basic experimental design is sound. In developing software to handle high throughput screening data, a fundamental requirement is to provide performance monitoring and error trapping facilities. Additional requirements are automatic data capture from instruments, on-line data reduction and analysis and transfer of results to central databases. As data volumes increase through effective high throughput screening, conventional interrogation methods become less appropriate and are being augmented by newer computing techniques referred to as knowledge mapping or database mining. Targeting cell surface receptors has been very successful as an approach to drug discovery. If the challenges of high throughput empirical screening are addressed effectively, cell surface receptors will provide new opportunities for improved therapy in the coming years.

Animals↗
PubMed2005

Inhaled bronchodilators for cystic fibrosis.

BACKGROUND: Recurrent wheeze and breathlessness are common in people with cystic fibrosis, and bronchodilators are commonly prescribed. Despite their wide-scale and often long-term use, there is limited objective evidence about their efficacy in cystic fibrosis. OBJECTIVES: To evaluate the effectiveness of inhaled bronchodilators in children and adults with cystic fibrosis. SEARCH STRATEGY: We searched the Cochrane Cystic Fibrosis and Genetic Disorders Group Trials Register comprising references identified from comprehensive electronic databases searches, and handsearches of relevant journals and abstract books of conference proceedings. Latest search of the Group's Trials Register: August 2005 SELECTION CRITERIA: Randomised or quasi-randomised trials comparing inhaled bronchodilators to placebo or another inhaled bronchodilator in people with CF, diagnosed clinically and by sweat or genetic testing and at all stages and severity of lung disease. DATA COLLECTION AND ANALYSIS: The authors independently extracted data and assessed trial quality. If data were missing, the primary author was contacted where possible. The data were subgrouped into classes of bronchodilator and for each class into short-term effects (less than one week) and long-term effects (greater or equal to one week). MAIN RESULTS: The search identified 43 references. Fourteen trials, with a total of 257 participants, were suitable for inclusion. The trials were all cross-over in design; in this case a meta-analysis was not possible. There were varied conclusions from the different trials, reflecting their heterogeneity. Compared to placebo, short-acting beta-2 agonists increased forced expiratory volume at one second (FEV(1)) in the short term in three out of five trials, and in the long-term increased peak expiratory flow rate in individuals who had been shown to have bronchial hyperreactivity or bronchodilator responsiveness or both. Compared to placebo, long-acting beta-2 agonists increased FEV(1) and forced expiratory flow between 25% and 75% of expiratory flow (FEF 25-75%) in the short term in participants known to have bronchodilator responsiveness, but produced inconsistent results in long-term trials. Short acting-anticholinergics had no consistent effect on lung function tests in either the short or the long term. We found no published trials of fenoterol, formoterol or tiotropium and the use of these agents in cystic fibrosis cannot be supported. AUTHORS' CONCLUSIONS: It was not possible to determine fully the effectiveness of inhaled bronchodilators in cystic fibrosis as a meta-analysis was not possible. However, both short and long-acting beta-2 agonists can be beneficial both in the short and long term in individuals with demonstrable bronchodilator responsiveness or bronchial hyperrresponsiveness.

Adrenergic beta-Agonists↗
PubMed2001

A comparative view of the new journal: Assessment.

The reference sections from all articles in the 1997 volumes of Assessment, Journal of Personality Assessment, and Psychological Assessment were entered into a database and analyzed. An article published in Assessment averaged almost 31 references. An article published in Journal of Personality Assessment contained an average of 33 references. Psychological Assessment averaged 38 references per article. The median age of the references in the three journals was 8 years with an interquartile range of 4 to 14 years. The Journal of Personality Assessment had the largest number of citations in this database of 5,316 references. Each of these received a relatively large number of their citations from articles published in the same journal (self-citations). Randomly selected articles from the 1997 volume of Assessment received fewer citations in the Social Science Citation Index than a similar set of articles from the other two journals. However, the data on Assessment, when compared with data available on other new scientific publications, suggests that Assessment is doing as well as other fledgling journals.

Bibliometrics↗
PubMed2001

Criminal DNA databases: the European situation.

In the last 5 years, a number of European countries have successfully introduced national databases holding the DNA profiles from suspected and convicted criminal offenders as well as from biological stain materials from unsolved crime cases. At present, DNA databases are fully or partially in operation in the UK, The Netherlands, Austria, Germany, Finland, Norway, Denmark, Switzerland and Sweden. Furthermore, in the other European countries, specific legislation will be enacted soon, or the introduction of such databases is being discussed to initiate a legislative process. Numerous differences exist regarding the criteria for a criminal offender to be included in the database, the storage periods and the possibility to remove database records, the possibility to keep reference samples from the offenders as long as their respective records are being held, and the role of judges in the process of entering a database record or to perform a database search. Nevertheless, harmonization has been achieved regarding the DNA information stored in national databases, and a European standard set of genetic systems has been recommended which is included either in part or completely in the DNA profiles of offenders and crime stains for all European databases. This facilitates the exchange of information from database records to allow the investigation of crime cases across national borders.

Confidentiality↗