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PubMed2005

The significance of agricultural vs. natural ecosystem pathways in temperate climates in assessments of long-term radiological impact.

Recent developments in performance assessment biosphere models have begun to emphasise the importance of natural accumulation pathways. In contrast to the agricultural pathways, the database for natural ecosystem pathways is less well developed, leading to a mismatch in quality of representations of the two types of system. At issue is the lack of reliable soil-plant and animal ingestion transfer factors for key radionuclides in natural ecosystems. The relative importance of the agricultural vs. natural ecosystem pathways is investigated here, in the context of a temperate site in present day, Eastern France. The BIOMASS Candidate Critical Group (CCG) methodology has been applied to map a set of eight candidate critical groups derived from the present-day societal context onto physical locations within a simple model of a river catchment system. The overall assessment model has been implemented using the Aquabios code. Annual individual dose to each of the CCGs has been calculated for each of the key radionuclides (79Se, 94Nb, 99Tc, 129I, 135Cs and 237Np) released to the valley aquifer and river. In addition to the traditional agricultural pathways, lifestyle groups exploiting natural habitats are explicitly addressed. Results show the susceptibility of different candidate critical groups to different radionuclides. A reference database typical of those employed in long-term performance assessment models is employed. Doses from external exposure (94Nb) and dust inhalation (237Np) are shown to dominate agricultural food consumption by factors of more than six, but, with the reference data set, foodstuffs obtained from natural ecosystems do not contribute significantly to critical group dose and, at most, show similar exposures to the agricultural pathways. This may lead to the conclusion that natural food can be ruled out of consideration in performance assessment models. However, systematic parametric sensitivity studies carried out on soil-plant and animal ingestion transfer factors restrict the validity of this observation and demonstrate the limitations of existing databases. Remaining uncertainties can be reduced by improving structural models for performance assessment and by better characterisation of sources of locally obtained foods. Improved characterisation of radionuclide accumulation in natural ecosystems in temperate as well as alternative future climate states should complement the modelling approach.

Agriculture↗

PubMed2006

Community hospitals--the place of local service provision in a modernising NHS: an integrative thematic literature review.

BACKGROUND: Recent developments within the United Kingdom's (UK) health care system have re-awakened interest in community hospitals (CHs) and their role in the provision of health care. This integrative literature review sought to identify and assess the current evidence base for CHs. METHODS: A range of electronic reference databases were searched from January 1984 to either December 2004 or February 2005: Medline, Embase, Web of Knowledge, BNI, CINAHL, HMIC, ASSIA, PsychInfo, SIGLE, Dissertation Abstracts, Cochrane Library, Kings Fund website, using both keywords and text words. Thematic analysis identified recurrent themes across the literature; narrative analyses were written for each theme, identifying unifying concepts and discrepant issues. RESULTS: The search strategy identified over 16,000 international references. We included papers of any study design focussing on hospitals in which care was led principally by general practitioners or nurses. Papers from developing countries were excluded. A review of titles revealed 641 potentially relevant references; abstract appraisal identified 161 references for review. During data extraction, a further 48 papers were excluded, leaving 113 papers in the final review. The most common methodological approaches were cross-sectional/descriptive studies, commentaries and expert opinion. There were few experimental studies, systematic reviews, economic studies or studies that reported on longer-term outcomes. The key themes identified were origin and location of CHs; their place in the continuum of care; services provided; effectiveness, efficiency and equity of CHs; and views of patients and staff. In general, there was a lack of robust evidence for the role of CHs, which is partly due to the ad hoc nature of their development and lack of clear strategic vision for their future. Evidence for the effectiveness and efficiency of the services provided was limited. Most people admitted to CHs appeared to be older, suggesting that admittance to CHs was age-related rather than condition-related. CONCLUSION: Overall the literature surveyed was long on opinion and short of robust studies on CHs. While lack of evidence on CHs does not imply lack of effect, there is an urgent need to develop a research agenda that addresses the key issues of health care delivery in the CH setting.

Health Services Research↗

PubMed2006

Exercise tissue Doppler echocardiography with strain rate imaging in healthy young individuals: feasibility, normal values and reproducibility.

PURPOSE OF THE STUDY: The study was done to determine the clinical feasibility and reproducibility of tissue Doppler echocardiography (TDE) with strain rate imaging (SRI) at rest and under physical exercise in healthy young individuals and to report normal values for parameters of regional myocardial function under exercise. METHODS: Forty-five young volunteers (age 9-29 years) underwent echocardiography with TDE/SRI at rest and during a bicycle exercise test (2 W/kg body weight). RESULTS: Velocities could be obtained in 93% of segments, whereas strain rate was measurable at least in 80% of segments. Inter- and intraobserver variability for measurement of velocities under exercise was 14% and 9%, respectively for strain rate 28% and 20%. Except for peak strain, values for all other parameters were higher during exercise with the clearest response in the left lateral and the right ventricular wall. CONCLUSIONS: (1) Tissue Doppler with strain rate imaging is a practical and robust method for assessment of regional function of both ventricles under exercise. (2) Systolic motion, local myocardial relaxation and contractility increased significantly under physical exercise. These normal values obtained from healthy young subjects can serve as a reference database for further clinical studies.

Adolescent↗

PubMedDate not supplied

[Normal bone mineral content levels determined by quantitative computer tomography (QCT) in the population of Moldavia].

UNLABELLED: To determine by QCT-BMD the normal osteodensitometric levels in the population of both sexes (18-80 years) from Moldavia districts. MATERIAL AND METHOD: The study used the BMD (bone mineral density) option of CT PACE GE-CGR (QCT) device which compares the CT levels in the area of interest restricted to the trabecular area of L1-L4 vertebrae with the values of a phantom with different hydroxyapatite concentrations. In order to develop a regional standard, an average of 10 both sexes subjects free of osteoporosis-generating diseases were investigated per each 5-year age group, age range 18 to 80 years, selected at random from the 8 districts of Moldavia. In both genders, data were plotted against age and were analysed with linear regression tests and the evolution curve (age-related) for each gender was drawn. RESULTS: The levels of score Z in both sexes were obtained. The obtained standard may be used as a reference database for the QCT investigation of the spine both in the male and female Romanian population.

Adolescent↗

PubMed2002

Inhaled corticosteroid effects on bone metabolism in asthma and mild chronic obstructive pulmonary disease.

BACKGROUND: Inhaled corticosteroids form the main therapy for asthma, but there is increasing concern about the potential systematic effects of long-term inhaled corticosteroids including their effect on bone metabolism and bone loss. OBJECTIVES: To determine the effect of inhaled corticosteroids use on biochemical markers of bone turnover, bone mineral density and the development of fractures. SEARCH STRATEGY: We searched the Cochrane Airways Group trials register, electronic reference databases, UK National Research Register, bibliographies of included studies, and contacted pharmaceutical companies. SELECTION CRITERIA: Randomised trials of the effect of inhaled steroid versus placebo on markers of bone function and metabolism, in adults with asthma or mild COPD. DATA COLLECTION AND ANALYSIS: Trial quality was assessed and data extracted from the papers included (2 reviewers per paper) and from additional data supplied by the authors. MAIN RESULTS: Of 438 references found, seven met the inclusion criteria. Three studies were in healthy subjects asthma or COPD. The patients were generally less than 60 years old and the male:female ratio was 2:1. There was no evidence of increased risk of loss of bone mineral density (BMD) or fractures. There was no significant change in osteocalcin at conventional doses of inhaled corticosteroids (Standardised Mean Difference [SMD] -0.34 (95% Confidence Interval [CI] -0.72, 0.04), although a statistically significant change was seen in those studies using experimental doses of inhaled steroid in excess of the doses recommended by the British Thoracic Society SMD 0.97 (95% CI -1.61, -0.34). A statistically significant change in parathyroid hormone seen in one small short trial (n=10, 6 weeks) may have been due to the trial design and outcome measurements used. REVIEWER'S CONCLUSIONS: In patients with asthma or mild COPD, there is no evidence of an effect of inhaled corticosteroid at conventional doses given for two or three years on BMD or vertebral fracture. Higher doses were associated with biochemical markers of increased bone turnover, but data on BMD and fractures at these doses are not available. There is a need for further, even longer term prospective studies of conventional and high doses of inhaled corticosteroids.

Administration, Inhalation↗

PubMed2005

RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank.

State-of-the-art methods based on CNS and CYANA were used to recalculate the nuclear magnetic resonance (NMR) solution structures of 500+ proteins for which coordinates and NMR restraints are available from the Protein Data Bank. Curated restraints were obtained from the BioMagResBank FRED database. Although the original NMR structures were determined by various methods, they all were recalculated by CNS and CYANA and refined subsequently by restrained molecular dynamics (CNS) in a hydrated environment. We present an extensive analysis of the results, in terms of various quality indicators generated by PROCHECK and WHAT_CHECK. On average, the quality indicators for packing and Ramachandran appearance moved one standard deviation closer to the mean of the reference database. The structural quality of the recalculated structures is discussed in relation to various parameters, including number of restraints per residue, NOE completeness and positional root mean square deviation (RMSD). Correlations between pairs of these quality indicators were generally low; for example, there is a weak correlation between the number of restraints per residue and the Ramachandran appearance according to WHAT_CHECK (r = 0.31). The set of recalculated coordinates constitutes a unified database of protein structures in which potential user- and software-dependent biases have been kept as small as possible. The database can be used by the structural biology community for further development of calculation protocols, validation tools, structure-based statistical approaches and modeling. The RECOORD database of recalculated structures is publicly available from http://www.ebi.ac.uk/msd/recoord.

Databases, Protein↗

PubMed1999

Acoustic characteristics of /s/ in adolescents.

The goal of the current study was to construct a reference database against which misarticulations of /s/ can be compared. Acoustic data for 26 typically speaking 9- to 15-year-olds were examined to resolve measurement issues in acoustic analyses, including alternative sampling points within the /s/ frication; the informativeness of linear versus Bark transformations of each of the 4 spectral moments of /s/ (Forrest, Weismer, Milenkovic, & Dougall, 1988); and measurement effects associated with linguistic context, age, and sex. Analysis of the reference data set indicates that acoustic characterization of /s/ is appropriately and optimally (a) obtained from the midpoint of /s/, (b) represented in linear scale, (c) reflected in summary statistics for the 1 st and 3rd spectral moments, (d) referenced to individual linguistic-phonetic contexts, (e) collapsed across the age range studied, and (f) described individually by sex.

Adolescent↗

PubMed1998

Plasma apolipoproteins A-I and B in survivors of myocardial infarction and in a control group.

The values of apolipoproteins (apo) A-I and B were determined in a population sample of hospital outpatients with a standardized method to verify if the cutpoints calculated in a cross-sectional study in the US are usable with other populations. We also tested the apolipoproteins' ability to discriminate between healthy people and survivors of myocardial infarction. In the studied population the apo A-I value corresponding to the HDL-cholesterol decisional centile is 1.12 g/L for males and 1.17 g/L for females; the apo B value corresponding to the LDL-cholesterol decisional centile is 1.23 g/L for males and 1.14 g/L for females. These values are quite close to the cutpoints proposed for the American population (1.20 g/L for both apolipoproteins). In comparison with the LDL- and HDL-cholesterol decisional concentrations, the cutpoints for apolipoproteins allow a correct classification of a greater percentage of postmyocardial infarction patients (16% higher for apo B and 5% for apo A-I). Standardized assays coupled with a reference database allow a better clinical use of apolipoprotein measurements.

Adult↗

PubMed2003

The Protein Information Resource.

The Protein Information Resource (PIR) is an integrated public resource of protein informatics that supports genomic and proteomic research and scientific discovery. PIR maintains the Protein Sequence Database (PSD), an annotated protein database containing over 283 000 sequences covering the entire taxonomic range. Family classification is used for sensitive identification, consistent annotation, and detection of annotation errors. The superfamily curation defines signature domain architecture and categorizes memberships to improve automated classification. To increase the amount of experimental annotation, the PIR has developed a bibliography system for literature searching, mapping, and user submission, and has conducted retrospective attribution of citations for experimental features. PIR also maintains NREF, a non-redundant reference database, and iProClass, an integrated database of protein family, function, and structure information. PIR-NREF provides a timely and comprehensive collection of protein sequences, currently consisting of more than 1 000 000 entries from PIR-PSD, SWISS-PROT, TrEMBL, RefSeq, GenPept, and PDB. The PIR web site (http://pir.georgetown.edu) connects data analysis tools to underlying databases for information retrieval and knowledge discovery, with functionalities for interactive queries, combinations of sequence and text searches, and sorting and visual exploration of search results. The FTP site provides free download for PSD and NREF biweekly releases and auxiliary databases and files.

Amino Acid Sequence↗

PubMed2006

UK reference data for the Hologic QDR Discovery dual-energy x ray absorptiometry scanner in healthy children and young adults aged 6-17 years.

BACKGROUND: The use and correct interpretation of bone densitometry measurements in paediatric patients relies on the availability of appropriate reference data. Ideally, such data should be matched for sex, chronological age, height, weight, pubertal development and ethnicity. AIM: To provide UK-specific reference data for the Hologic QDR Discovery dual-energy x ray absorptiometry (DXA) scanners. METHODS: Healthy, Caucasian children aged 5-18 years were recruited from local schools, colleges, general practitioner surgeries and staff from the University of Manchester, Manchester, UK. Suitable participants had DXA measurements taken of the lumbar spine, hip and total body. Sex-specific reference centile curves for bone mineral apparent density (BMAD; spine and femoral neck) are provided, using the approach suggested by Mølgaard et al. to interpret the scans. LMS (lambda, mu, varsigma) tables for calculation of individual standard deviation scores (SDSs) were produced; a weblink is provided to these tables to allow calculation of an individual child's SDSs. RESULTS: The total study population consisted of 442 participants (239 male). The total numbers of scans available for analysis were 431 of the lumbar spine, 426 of the total body and 393 of the proximal femur. Data are provided for clinical interpretation of the spine and femoral neck scans based on BMAD (g/cm3), which reduces the size dependence of DXA areal bone mineral density (g/cm2). The spine and total-body data are also presented for interpretation of results using the approach suggested by Mølgaard et al. CONCLUSIONS: This article provides the first sex-specific and ethnicity-specific reference databases for UK, which should allow the clinician to assess bone mineral density in paediatric patients, measured by the Hologic QDR Discovery DXA scanner.

Absorptiometry, Photon↗

PubMed1996

Are convenience DNA samples significantly different?

In this paper, the issue of whether DNA databases collected by different convenience sampling methods are significantly different statistically is investigated. Testing the null hypothesis that the population probability or frequency distributions of DNA profiles under different sampling methods are the same is of interest in this investigation. Some statistical analyses are conducted on the single-locus VNTR databases collected from different sources by the Hong Kong Government Laboratory. The bootstrap, Monte Carlo simulation and significance tests including the Pearson's chi-squared, likelihood ratio, and Kolmogorov-Smirnov two-sample statistics are employed for testing the hypothesis. The results are promising that no probability values of the tests are smaller than 5%. In other words, there is not enough evidence to reject the null hypothesis at the 5% level, which provides more confidence for using the VNTR reference databases commonly collected by convenience sampling.

DNA↗

PubMedDate not supplied

[Can primary care physicians use the ICD-9-MC? An evaluation of the quality of diagnosis coding in computerized medical records].

OBJECTIVES: To determine the completeness and accuracy of ICD-9-CM codes allocated by primary health care physicians in their computerized medical records and evaluate the effects of improvement procedures. METHODS: The codes of 87,806 patients assigned to 56 primary care physicians in the Basque National Health Service in Spain, were evaluated 3 times over a 1-year period according to the following criteria: correspondence to a valid ICD-9-CM code, agreement between diagnosis and code, and the percentage of visits with an unspecified reason for consultation. Finally, the mean number of unique diagnoses and rates of diagnostic groups in the 84,136 patients that remained with the same physician for a minimum of 6 months were contrasted with another previously registered morbidity database. Two interventions were performed to improve coding: detected errors were corrected centrally and physicians were assessed and given information on their individual results. RESULTS: Diagnoses lacking an ICD-9-DIC code decreased from 59% in the first assessment to 2% at the end of the study period. The percentage of coding mistakes (discrepancies in episode diagnosis and ICD-9-CM code) decreased from 17% to 3%. The mean annual number of diagnoses per patient was slightly lower than that in the reference database (2.26 versus 2.43). The same result was observed in the rates of some diagnostic groups. CONCLUSIONS: Primary care doctors can achieve a high degree of quality in ICD-9-CM diagnosis coding. Implementing procedures for evaluating coding, rectifying mistakes, and providing information to physicians markedly improved the initial results.

Cross-Sectional Studies↗

PubMed2004

Alterations in bone characteristics associated with glycemic control in adolescents with type 1 diabetes mellitus.

OBJECTIVE: To determine whether bone characteristics in adolescents with type 1 diabetes mellitus (DM) are influenced by blood glucose regulation and disease duration. The subjects were adolescents with type 1 DM (n=55) recruited from the University of Utah's Primary Children's Pediatric Diabetes Treatment Center. A reference database consisting of 95 healthy adolescents from the same geographic area was used for comparison.Study design Measurements of the tibia by peripheral quantitative computed tomography were made to assess cortical and trabecular bone characteristics. Hip, spine, and whole body characteristics were measured by dual-energy x-ray absorptiometry. Height, weight, health histories, Tanner stage, disease duration, insulin regimen, and glycosylated hemoglobin values were recorded. RESULTS: Age, maturation, and body size and composition values were similar between the subjects with type 1 DM and reference. Subjects with type 1 DM had lower tibia trabecular and femoral neck density and whole body mineral content and density. The mean glycosylated hemoglobin value was inversely related to tibia trabecular bone density (R(2)=-0.30) and whole body bone mineral content (R(2)=-0.25) and accounted for 3.0% to 8.9% of the variance. CONCLUSIONS: Altered bone mineral acquisition in adolescents with type 1 DM may limit peak bone mass acquisition and increase the risk of osteoporosis in later life.

Absorptiometry, Photon↗

PubMed2004

DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data.

The DICHROWEB web server enables on-line analyses of circular dichroism (CD) spectroscopic data, providing calculated secondary structure content and graphical analyses comparing calculated structures and experimental data. The server is located at http://www.cryst.bbk.ac.uk/cdweb and may be accessed via a password-limited user ID, available upon completion of a registration form. The server facilitates analyses using five popular algorithms and (currently) seven different reference databases by accepting data in a user-friendly manner in a wide range of formats, including those output by both commercial CD instruments and synchrotron radiation-based circular dichroism beamlines, as well as those produced by spectral processing software packages. It produces as output calculated secondary structures, a goodness-of-fit parameter for the analyses, and tabular and graphical displays of experimental, calculated and difference spectra. The web pages associated with the server provide information on CD spectroscopic methods and terms, literature references and aids for interpreting the analysis results.

Algorithms↗

PubMed2006

Hungarian mtDNA population databases from Budapest and the Baranya county Roma.

To facilitate forensic mtDNA testing in Hungary, we have generated control region databases for two Hungarian populations: 211 individuals were sampled from the urban Budapest population and 208 individuals were sampled from a Romani ("gypsy") population in Baranya county. Sequences were generated using a highly redundant approach to minimize potential database errors. The Budapest population had high sequence diversity with 180 lineages, 183 polymorphic positions, and a random match probability of 1%. In contrast, the Romani population exhibited low sequence diversity, with only 56 lineages, 109 segregating sites, and a random match probability of 8.8%. The mtDNA haplogroup compositions of the two populations were also distinct, with the large proportion of haplogroup M samples (35%) in the Roma the most obvious difference between the two populations. These factors highlight the importance of considering population structure when generating reference databases for forensic testing purposes. Comparisons between our Romani population sample and other published data indicate the need for heightened caution when sampling and using mtDNA databases of small endogamous populations. The Romani populations that we compared showed significant departures from genetic uniformity.

DNA, Mitochondrial↗

PubMed2002

RiceGAAS: an automated annotation system and database for rice genome sequence.

An extensive effort of the International Rice Genome Sequencing Project (IRGSP) has resulted in rapid accumulation of genome sequence, and >137 Mb has already been made available to the public domain as of August 2001. This requires a high-throughput annotation scheme to extract biologically useful and timely information from the sequence data on a regular basis. A new automated annotation system and database called Rice Genome Automated Annotation System (RiceGAAS) has been developed to execute a reliable and up-to-date analysis of the genome sequence as well as to store and retrieve the results of annotation. The system has the following functional features: (i) collection of rice genome sequences from GenBank; (ii) execution of gene prediction and homology search programs; (iii) integration of results from various analyses and automatic interpretation of coding regions; (iv) re-execution of analysis, integration and automatic interpretation with the latest entries in reference databases; (v) integrated visualization of the stored data using web-based graphical view. RiceGAAS also has a data submission mechanism that allows public users to perform fully automated annotation of their own sequences. The system can be accessed at http://RiceGAAS.dna.affrc.go.jp/.

Automation↗

PubMed2005

Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships.

MOTIVATION: Given that association and dissociation of protein molecules is crucial in most biological processes several in silico methods have been recently developed to predict protein-protein interactions. Structural evidence has shown that usually interacting pairs of close homologs (interologs) physically interact in the same way. Moreover, conservation of an interaction depends on the conservation of the interface between interacting partners. In this article we make use of both, structural similarities among domains of known interacting proteins found in the Database of Interacting Proteins (DIP) and conservation of pairs of sequence patches involved in protein-protein interfaces to predict putative protein interaction pairs. RESULTS: We have obtained a large amount of putative protein-protein interaction (approximately 130,000). The list is independent from other techniques both experimental and theoretical. We separated the list of predictions into three sets according to their relationship with known interacting proteins found in DIP. For each set, only a small fraction of the predicted protein pairs could be independently validated by cross checking with the Human Protein Reference Database (HPRD). The fraction of validated protein pairs was always larger than that expected by using random protein pairs. Furthermore, a correlation map of interacting protein pairs was calculated with respect to molecular function, as defined in the Gene Ontology database. It shows good consistency of the predicted interactions with data in the HPRD database. The intersection between the lists of interactions of other methods and ours produces a network of potentially high-confidence interactions.

Algorithms↗

PubMed1998

Updated data on proximal femur bone mineral levels of US adults.

This paper describes data on bone mineral levels in the proximal femur of US adults based on the nationally representative sample examined during both phases of the third National Health and Nutrition Examination Survey (NHANES III, 1988-94), and updates data previously presented from phase 1 only. The data were collected from 14,646 men and women aged 20 years and older using dual-energy X-ray absorptiometry, and included bone mineral density (BMD), bone mineral content (BMC) and area of bone scanned in four selected regions of interest (ROI) in the proximal femur: femur neck, trochanter, intertrochanter and total. These variables are provided separately by age and sex for non-Hispanic whites (NHW), non-Hispanic blacks (NHB) and Mexican Americans (MA). NHW in the southern United States had slightly lower BMD levels than NHW in other US regions, but these differences were not sufficiently large to prevent pooling of the data. The updated data provide valuable reference data on femur bone mineral levels of noninstitutionalized adults. The updated data on BMD for the total femur ROI of NHW have been selected as the reference database for femur standardization efforts by the International Committee on Standards in Bone Measurements.

Absorptiometry, Photon↗