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Comparison of clinical prediction rules for management of pharyngitis in settings with limited resources.

OBJECTIVE: To compare the effectiveness of several clinical prediction rules for culture-positive streptococcal pharyngitis in a single group of patients in a setting in which clinicians routinely treat all cases of pharyngitis presumptively, without laboratory data. STUDY DESIGN: A MEDLINE search identified clinical prediction rules for streptococcal pharyngitis in children. Each rule was applied analytically to data from 410 children in Cairo, Egypt with clinical pharyngitis, in whom throat cultures were performed. The diagnostic effectiveness of these rules for predicting a positive culture were assessed and compared. RESULTS: Seven prediction rules were identified. Of these 7 rules, 4 were developed in North American children, 1 was recommended by the World Health Organization (WHO), and 2 were developed in Egypt. In the Cairo children, the WHO rule was the least sensitive, at 12%. The 6 other rules had sensitivities ranging from 81% to 99% and specificities ranging from 4% to 40%; 2 rules seemed to be effective, with diagnostic odds ratios of 5.2 and 6.1. CONCLUSIONS: The prediction rules demonstrated variable diagnostic effectiveness in the Egyptian children. Without laboratory testing, 2 clinical rules detected > 90% of cases of pharyngitis with positive culture for group A streptococcus and reduced overtreatment of culture-negative cases by approximately 40%. Selected clinical prediction rules have useful characteristics in settings of limited resources and need further validation.

Ampicillin↗

Multivariate data analysis of NMR data.

Multivariate methods based on principal components (PCA and PLS) have been used to reduce NMR spectral information, to predict NMR parameters of complicated structures, and to relate shift data sets to dependent descriptors of biological significance. Noise reduction and elimination of instrumental artifacts are easily performed on 2D NMR data. Configurational classification of triterpenes and shift predictions in disubstituted benzenes can be obtained using PCA and PLS analysis. Finally, the shift predictions of tripeptides from descriptors of amino acids open the possibility of automatic analysis of multidimensional data of complex structures.

Amino Acid Sequence↗

Three-dimensional H-1 MR spectroscopic imaging of the in situ human prostate with high (0.24-0.7-cm3) spatial resolution.

PURPOSE: To evaluate if three-dimensional hydrogen-1 magnetic resonance spectroscopic imaging (3D MRSI) when combined with a clinical MR imaging examination could discriminate prostatic adenocarcinoma from normal prostatic zonal anatomy and benign prostatic hyperplasia (BPH) on the basis of observable metabolite levels. MATERIALS AND METHODS: Combined phased-array, endorectal MR imaging and 3D MRSI was performed in nine young healthy volunteers, five patients with BPH, and 85 patients with prostate cancer and BPH. Volume MR imaging and 3D MRSI data were analytically corrected for the reception profile of the endorectal and pelvic phased-array coils, aligned with the MR imaging data, and compared with postoperative pathologic histology findings. RESULTS: Statistically significant variations in metabolite levels with prostatic zonal anatomy, age, and pathologic condition were detected with a 3D MRSI examination added to a clinical MR imaging examination. Significantly higher choline levels and significantly lower citrate levels were observed in regions of cancer compared with BPH and normal peripheral zone tissues. The ratio (choline + creatine/citrate) in regions of cancer (2.1 +/- 1.3 [standard deviation]) had no overlap with normal peripheral zone values and minimal overlap with BPH values (0.61 +/- 0.21). An estimate of the spatial extent of prostate cancer was determined by generating metabolite images in which this metabolite ratio significantly exceeded normal peripheral zone values in multiple contiguous sections. CONCLUSION: These results suggest that a 3D MRSI examination added to a clinical MR imaging examination may help define the presence and spatial extent of prostate cancer.

Adenocarcinoma↗

Flexible meta-regression functions for modeling aggregate dose-response data, with an application to alcohol and mortality.

In this paper, the authors describe fractional polynomials and cubic splines with which to represent smooth dose-response relations in summarizing meta-analytical aggregate data. Use of these two curve-fitting families can help prevent the problems arising from inappropriate linearity assumptions. These methods are illustrated in the problem of estimating the shape of the dose-response curve between alcohol consumption and all-cause mortality risk. The authors considered aggregate data from 29 cohort studies investigating this issue (1966-2000). J-shaped curves with a nadir at approximately 5-7 g/day of alcohol consumption and a last protective dose of 47-60 g/day were consistently obtained from fractional polynomials and cubic splines. The authors conclude that both of the curve-fitting families are useful tools with which to explore dose-response epidemiologic questions by means of meta-analytical approaches, especially when important nonlinearity is anticipated.

Alcohol Drinking↗

AutoScan: an automated workstation for rapid determination of mass and tandem mass spectrometry conditions for quantitative bioanalytical mass spectrometry.

An automated flow injection analysis (FIA) mass spectrometry system (AutoScan) was developed to allow rapid unattended determination of optimal conditions during mass (ms) and tandem mass spectrometry (ms/ms) on new chemical entities (NCEs) arranged in 96-well plates. The 96-well plate is placed on the deck of a modified Gilson Multiprobe autosampler for injection into a PE Sciex API 2000 triple quadrupole mass spectrometer. A customized software interface is used to create the necessary scan experiments by associating each 96-well plate of NCEs to be scanned with an index file containing data on the identity of each analyte and its expected molecular weight. Analytes are injected four at a time into a custom injection manifold and conventional mass spectra are acquired in both polarities (+/-) using an alternating positive/negative Q1 scan function. The software determines the optimal polarity and definitive precursor ion for all analytes and uses the results to build the injection sequence for product ion scanning. The samples are automatically re-injected under MS/MS conditions, and product ion scans that loop among different collision energies are collected for each analyte. The resulting data are processed automatically and the optimal MS/MS transitions for each analyte are selected. A color-coded graphical interface facilitates data review. Any unusual ion transitions or transposition errors made during plate preparation are noted and corrected. Complete MS and MS/MS conditions are obtained for 96 compounds in about one hour and the resulting data are available for download as sample control injection sequence files.

Automation↗

Continuous aqueous phase extraction of proteins: automated on-line monitoring of fumarase activity and protein concentration.

Automated assay techniques are described for on-line measurements of fumarase activity and total protein concentration, including in-line sample dilution and sample multiplexing during continuous aqueous phase extraction. Fumarase was determined by following the conversion of L-malate to fumurate at a wavelength of 250 nm, while the protein assay was based on the Biuret reaction. Actual assay times of 2 and 4 min were achieved for the fumarase and protein measurements, respectively, with an effective measurement cycle time of 2 min. Standard deviations of c. 3.2 and 2% of the measured values were calculated for the enzyme and protein values, respectively. The assay system was coupled to a computer to allow on-line data visualization and storage.

Automation↗

Validity of international, time trend, and migrant studies of dietary factors and disease risk.

A linear form relative risk model is used to identify circumstances in which various types of aggregate data lead to valid inferences on relative risk parameters. Upon making a random effects assumption, international or time trend data can lead to appropriate relative risk parameter estimation using iteratively reweighted least-squares procedures. Adequate confounding factor control, however, will typically require data on the distribution of confounding factors in each country or time period. For a simple interpretation of relative risk parameters one may also require data on the joint distribution of primary and confounding factors in each country or time period. Hence disease rate data need to be supplemented by dietary and risk factor survey data in order to avoid confounding bias. Measurement error in individual dietary assessment may, however, limit the ability to quantify the dependence of relative risk on dietary factors, unless the relative risk function is approximately linear in the dietary factors of interest. Most studies of migrant populations involve a comparison of migrant mortality rates with those of their countries of emigration and immigration, with little or no data collection on the dietary habits and risk factors of the migrants themselves. The potential of more comprehensive aggregate data and analytic migrant studies in the diet and disease area is briefly indicated. These issues and methods are illustrated using various types of data pertinent to the association between dietary fat and breast cancer.

Breast Neoplasms↗

Effects of surface finish on indentation modulus and hardness of dental composite restoratives.

OBJECTIVES: The depth-sensing micro-indentation testing was recently introduced for the characterization of dental composites. One of the critical issues raised was the possible influence of surface finish on material properties. The aim of this study was to investigate the effects of surface finish on the indentation modulus and micro-hardness of resin-based dental composite materials. METHODS: The materials used included minifill (Z100, 3M ESPE), microfill (A110, 3M ESPE) and poly-acid modified (F2000, 3M ESPE) composites. The specimens were polished successively using SiC grinding papers of different grit size and diamond suspensions to achieve varying surface roughness. The arithmetic mean of the roughness (R(a)) was measured using profilometry. In the depth-sensing micro-indentation test, specimens (n=7) were indented to 10N with Vickers indenter and the load-displacement (P-h) data was obtained using a universal testing system. The indentation modulus (E(in)) and hardness (H) were then computed using the developed analytical solutions. Data was analyzed using ANOVA/post-hoc Scheffe's test at significance level 0.05. RESULTS: The polished specimens had surface roughness ranging from 0.02 to 0.81 microm. The roughness of F2000 was significantly higher than A110 and Z100. The E(in) and H for Z100 ranged from 14.02 to 14.83GPa and 1.18 to 1.27 GPa, respectively. E(in) for F2000 and A110 ranged from 12.25 to 13.82 GPa and 5.26 to 5.52 GPa and hardness ranged from 0.89 to 0.98 GPa and 0.52 to 0.55 GPa, respectively. SIGNIFICANCE: The indentation modulus and hardness of dental composite restoratives were independent of the surface finish provided indenter penetration is sufficiently deep (h(max)/R(a)>30).

Compomers↗

Evaluation of protective shielding thickness for diagnostic radiology rooms: theory and computer simulation.

This work presents the development and evaluation using modern techniques to calculate radiation protection barriers in clinical radiographic facilities. Our methodology uses realistic primary and scattered spectra. The primary spectra were computer simulated using a waveform generalization and a semiempirical model (the Tucker-Barnes-Chakraborty model). The scattered spectra were obtained from published data. An analytical function was used to produce attenuation curves from polychromatic radiation for specified kVp, waveform, and filtration. The results of this analytical function are given in ambient dose equivalent units. The attenuation curves were obtained by application of Archer's model to computer simulation data. The parameters for the best fit to the model using primary and secondary radiation data from different radiographic procedures were determined. They resulted in an optimized model for shielding calculation for any radiographic room. The shielding costs were about 50% lower than those calculated using the traditional method based on Report No. 49 of the National Council on Radiation Protection and Measurements.

Calibration↗

GOLD.db: genomics of lipid-associated disorders database.

BACKGROUND: The GOLD.db (Genomics of Lipid-Associated Disorders Database) was developed to address the need for integrating disparate information on the function and properties of genes and their products that are particularly relevant to the biology, diagnosis management, treatment, and prevention of lipid-associated disorders. DESCRIPTION: The GOLD.db http://gold.tugraz.at provides a reference for pathways and information about the relevant genes and proteins in an efficiently organized way. The main focus was to provide biological pathways with image maps and visual pathway information for lipid metabolism and obesity-related research. This database provides also the possibility to map gene expression data individually to each pathway. Gene expression at different experimental conditions can be viewed sequentially in context of the pathway. Related large scale gene expression data sets were provided and can be searched for specific genes to integrate information regarding their expression levels in different studies and conditions. Analytic and data mining tools, reagents, protocols, references, and links to relevant genomic resources were included in the database. Finally, the usability of the database was demonstrated using an example about the regulation of Pten mRNA during adipocyte differentiation in the context of relevant pathways. CONCLUSIONS: The GOLD.db will be a valuable tool that allow researchers to efficiently analyze patterns of gene expression and to display them in a variety of useful and informative ways, allowing outside researchers to perform queries pertaining to gene expression results in the context of biological processes and pathways.

Adipocytes↗

Data base management systems for evaluation of analytical procedures.

The present paper gives a short introduction to data base management systems, and their application in the clinical laboratory for evaluating the quality of analytical procedures. Two applications based on the MIMER relational data base management system are described in some detail: An internal quality control data base under development at the clinical chemistry laboratory of the University Hospital in Uppsala, and a data base system for external quality assessment developed in a previous NORDKEM project.

Chemistry, Clinical↗

caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid.

MOTIVATION: The complexity of cancer is prompting researchers to find new ways to synthesize information from diverse data sources and to carry out coordinated research efforts that span multiple institutions. There is a need for standard applications, common data models, and software infrastructure to enable more efficient access to and sharing of distributed computational resources in cancer research. To address this need the National Cancer Institute (NCI) has initiated a national-scale effort, called the cancer Biomedical Informatics Grid (caBIGtrade mark), to develop a federation of interoperable research information systems. RESULTS: At the heart of the caBIG approach to federated interoperability effort is a Grid middleware infrastructure, called caGrid. In this paper we describe the caGrid framework and its current implementation, caGrid version 0.5. caGrid is a model-driven and service-oriented architecture that synthesizes and extends a number of technologies to provide a standardized framework for the advertising, discovery, and invocation of data and analytical resources. We expect caGrid to greatly facilitate the launch and ongoing management of coordinated cancer research studies involving multiple institutions, to provide the ability to manage and securely share information and analytic resources, and to spur a new generation of research applications that empower researchers to take a more integrative, trans-domain approach to data mining and analysis. AVAILABILITY: The caGrid version 0.5 release can be downloaded from https://cabig.nci.nih.gov/workspaces/Architecture/caGrid/. The operational test bed Grid can be accessed through the client included in the release, or through the caGrid-browser web application http://cagrid-browser.nci.nih.gov.

Biomarkers, Tumor↗

A clinical view of analytical goals in clinical biochemistry.

The analytical goals inferred desirable by a group of clinicians for the imprecisions of a wide range of analytes have been studied by survey. The goals required have not in general become more stringent in the past decade and are not as demanding as those promulgated by laboratory professionals. Clinical biochemistry laboratories can now attain analytical imprecisions which satisfy the general demands of clinicians except for analyses of calcium and of low levels of glucose. The lack of published data on analytical goals does not allow wide comparison of criteria for performance standards with the results of this study.

Attitude of Health Personnel↗

Report of the Spanish Gaucher's disease registry: clinical and genetic characteristics.

BACKGROUND AND OBJECTIVES: Since 1993 the demographic, clinical, analytical, genetic and follow-up data of Spanish patients with Gaucher's disease (GD) have been collected in an anonymous national database. Some statistical analyses of these data are reported concerning the distribution, clinical and genetic characteristics of GD in Spain and the response to enzyme replacement therapy (ERT) is evaluated. DESIGN AND METHODS: We performed a cohort study in Spanish GD patients by national inquiry, submitted by mail to 75 Spanish hospitals (over 300 beds) directed to internal medicine, hematology and pediatric departments. The questionnaire included 30 questions (gender, height, weight, date of birth, date of diagnosis, abode and number of relatives affected, bone crises, neurologic symptoms, other symptoms, liver and spleen size, hemoglobin, leukocyte and platelet count, tartrate resistant acid phosphatase, ALT/AST, chitotrioxidase activity, total plasma cholesterol, triglycerides, high density lipoprotein cholesterol, enzymatic activity of acid -glycosides, mutation, X-ray examination, magnetic resonance imaging-MRI-evaluation, spleen removal, and orthopedic procedures (ERT, date of first infusion). Each case with a presumed diagnosis was considered an enrolled patient. Written informed consent was obtained from all patients. The cases without enzymatic or genetic diagnosis were studied in a reference laboratory (the same for all the samples). Clinical status was evaluated by Zimran's severity score index. The enzymatic activity of acid -glycosides was determined in cellular extracts of peripheral blood granulocytes by a fluorescent method using an artificial substrate (4-methyl-umbelliferyl -D-glycoside). Polymerase chain reaction (PCR) molecular analysis was performed in DNA samples to characterize the mutations (N370S, L444P, IVS2+1, 84GG, D409H, R463C and G377S) of the glycoside genes. Two groups were created according to age at diagnosis: children under 15 years and adults, in order to evaluate clinical, genetics and follow-up. Effectiveness of ERT was evaluated using objective parameters (hemoglobin, platelets, liver and spleen size, skeletal lesions), before and after therapy. In patients under ERT, quality of life (QOL) was assessed by a SF-36 modified inquiry, including 22 questions. Statistical analysis including descriptive and frequency distribution for each variable was performed, the ANOVA test was used to identify differences between groups. Paired t-tests (before and during therapy) were carried out. The degree of linear association among measured variables was estimated by Pearson's correlation. RESULTS: By December 1999 one hundred and fifty-five patients from 117 families had been included from 66 Spanish Hospitals; the inquiry was complete for 114 patients. Mean age at diagnosis: 24.0+/-16.9 years, M/F: 72/83. No symptoms were present at diagnosis in 19.3%; visceral disease was present in 95.6% and bone disease in 62.4%. Hemoglobin levels, leukocyte and platelet counts were below the normal range in 62.3% of cases. Higher acid phosphatase levels were observed in 99% of cases; biochemical liver dysfunction tests were found in 42.9%. The test for acid glycosidase showed a marked decrease in enzymatic activity. Morphologic documentation (spleen or liver tissue, bone marrow biopsy or aspirate) of GD was obtained in 71% of the patients. The most frequent mutations observed were N370S (46.3% of the alleles detected), and L444P (18.5%). In 18.7% of the cases the disease was stable or progressing slightly; in 23.8% the spleen had been removed between 1-14 years after diagnosis and 60.6% were under ERT. Children showed both greater liver enlargement and higher SSI (p = 0.0001). There was a correlation between SSI and clinical or analytical data in adults patients for spleen size (Z: 3.142; CI: 0. 173-0.637; p= 0.0017). In 35 patients on ERT, clinical and analytic data improved as did self-evaluated QOL (p< 0.0001). (A

Adolescent↗

Time course solutions of the Sax-Markov binary eurejoining/misrejoining model of DNA double-strand breaks.

The Sax-Markov binary eurejoining/misrejoining (SMBE) model is a stochastic representation of Sax's breakage-and-reunion mechanism of misrejoining DNA double-strand breaks (DSBs). In this model, to approximate DSB misrejoining probabilities that decrease with increasing distance, the nucleus is treated as a collection of eta isolated nuclear subvolumes called sites; DSB free ends within the same site interact with a probability that is independent of distance, and DSB free ends within different sites never interact. In our previous work, SMBE steady-state solutions were used to estimate eta from a combination of high-dose PFGE (pulsed-field gel electrophoresis) data and moderate-dose chromosomal aberration data. Here, analytic SMBE transient solutions (i.e., time courses of DSBs and misrejoinings) are derived and used to estimate eta from various sets of misrejoining DSB kinetic data. The time courses are multiexponentials with rate constants kappa, 6kappa, 15kappa, ... j(2j-1)kappa corresponding to different nuclear site states and not different types of DSBs. For example, the kappa component corresponds to nuclear sites with two DSB free ends and thus only one possible rejoining interaction, and the 6kappa component corresponds to sites with four DSB free ends and thus six (four choose two) potential rejoining interactions--four of these six potential interactions lead to a final state of two misrejoinings and the other two of six lead to a final state of correct repair (unrejoinable DSBs are not represented in the SMBE model). The SMBE time course solutions provide site number estimates that fall in the range of eta approximately equals 10-100 for premature chromosome condensation (PCC) data and eta approximately equals 1,000 for PFGE data.

DNA↗

Positive natural selection in the human lineage.

Positive natural selection is the force that drives the increase in prevalence of advantageous traits, and it has played a central role in our development as a species. Until recently, the study of natural selection in humans has largely been restricted to comparing individual candidate genes to theoretical expectations. The advent of genome-wide sequence and polymorphism data brings fundamental new tools to the study of natural selection. It is now possible to identify new candidates for selection and to reevaluate previous claims by comparison with empirical distributions of DNA sequence variation across the human genome and among populations. The flood of data and analytical methods, however, raises many new challenges. Here, we review approaches to detect positive natural selection, describe results from recent analyses of genome-wide data, and discuss the prospects and challenges ahead as we expand our understanding of the role of natural selection in shaping the human genome.

Alleles↗

Review of guidelines for good practice in decision-analytic modelling in health technology assessment.

OBJECTIVES: To identify existing guidelines and develop a synthesised guideline plus accompanying checklist. In addition to provide guidance on key theoretical, methodological and practical issues and consider the implications of this research for what might be expected of future decision-analytic models. DATA SOURCES: Electronic databases. REVIEW METHODS: A systematic review of existing good practice guidelines was undertaken to identify and summarise guidelines currently available for assessing the quality of decision-analytic models that have been undertaken for health technology assessment. A synthesised good practice guidance and accompanying checklist was developed. Two specific methods areas in decision modelling were considered. The first method's topic is the identification of parameter estimates from published literature. Parameter searches were developed and piloted using a case-study model. The second topic relates to bias in parameter estimates; that is, how to adjust estimates of treatment effect from observational studies where there are risks of selection bias. A systematic literature review was conducted to identify those studies looking at quantification of bias in parameter estimates and the implication of this bias. RESULTS: Fifteen studies met the inclusion criteria and were reviewed and consolidated into a single set of brief statements of good practice. From this, a checklist was developed and applied to three independent decision-analytic models. Although the checklist provided excellent guidance on some key issues for model evaluation, it was too general to pick up on the specific nuances of each model. The searches that were developed helped to identify important data for inclusion in the model. However, the quality of life searches proved to be problematic: the published search filters did not focus on those measures specific to cost-effectiveness analysis and although the strategies developed as part of this project were more successful few data were found. Of the 11 studies meeting the criteria on the effect of selection bias, five concluded that a non-randomised trial design is associated with bias and six studies found 'similar' estimates of treatment effects from observational studies or non-randomised clinical trials and randomised controlled trials (RCTs). One purpose of developing the synthesised guideline and checklist was to provide a framework for critical appraisal by the various parties involved in the health technology assessment process. First, the guideline and checklist can be used by groups that are reviewing other analysts' models and, secondly, the guideline and checklist could be used by the various analysts as they develop their models (to use it as a check on how they are developing and reporting their analyses). The Expert Advisory Group (EAG) that was convened to discuss the potential role of the guidance and checklist felt that, in general, the guidance and checklist would be a useful tool, although the checklist is not meant to be used exclusively to determine a model's quality, and so should not be used as a substitute for critical appraisal. CONCLUSIONS: The review of current guidelines showed that although authors may provide a consistent message regarding some aspects of modelling, in other areas conflicting attributes are presented in different guidelines. In general, the checklist appears to perform well, in terms of identifying those aspects of the model that should be of particular concern to the reader. The checklist cannot, however, provide answers to the appropriateness of the model structure and structural assumptions, as these may be seen as a general problem with generic checklists and do not reflect any shortcoming with the synthesised guidance and checklist developed here. The assessment of the checklist, as well as feedback from the EAG, indicated the importance of its use in conjunction with a more general checklist or guidelines on economic evaluation. Further methods research into the following areas would be valuable: the quantification of selection bias in non-controlled studies and in controlled observational studies; the level of bias in the different non-RCT study designs; a comparison of results from RCTs with those from other non-randomised studies; assessment of the strengths and weaknesses of alternative ways to adjust for bias in a decision model; and how to prioritise searching for parameter estimates.

Benchmarking↗

Heart failure. A decision analytic analysis of New Zealand data using the published results of the SOLVD Treatment Trial. Studies of Left Ventricular Dysfunction.

This study sought to evaluate the changes in direct medical costs and life-years gained or lost by adding enalapril to conventional treatment (digoxin and diuretics) for heart failure (HF). The published results of the Studies of Left Ventricular Dysfunction (SOLVD) Treatment Trial, and a decision analytical model developed by the University of Pennsylvania, were used in combination with New Zealand data to undertake the evaluation. All costs were measured in 1993 New Zealand dollars ($NZ) [$NZ1 = $US0.5509, September 1993]. Potential net cost savings per patient treated over a 4-year period were $NZ652 together with an additional 2 months of life gained. If these individual potential cost savings are extended to the New Zealand population who have HF (but are at present not receiving an ACE inhibitor) then $NZ6 517 000 in discounted health sector costs could be avoided. The model was sensitive to changes in the price of enalapril, to estimates of the population with HF, the percentage of the population with HF treated with enalapril, and to hospital unit costs for nonfatal cases of HF. The study demonstrated that the addition of enalapril to the conventional treatment of HF was cost effective when compared with conventional medical therapy alone.

Angiotensin-Converting Enzyme Inhibitors↗