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At least 1,153 records · Page 64Linked to original sources
PubMed2004

Methodology for lognormal modelling of malignant pleural mesothelioma survival time distributions: a study of 5580 case histories from Europe and USA.

A truncated left-censored and right-censored lognormal model has been validated for representing pleural mesothelioma survival times in the range 5-200 weeks for data subsets grouped by age for males, 40-49, 50-59, 60-69, 70-79 and 80+ years and for all ages combined for females. The cases available for study were from Europe and USA and totalled 5580. This is larger than any other pleural mesothelioma cohort accrued for study. The methodology describes the computation of reference baseline probabilities, 5-200 weeks, which can be used in clinical trials to assess results of future promising treatment methods. This study is an extension of previous lognormal modelling by Mould et al (2002 Phys. Med. Biol. 47 3893-924) to predict long-term cancer survival from short-term data where the proportion cured is denoted by C and the uncured proportion, which can be represented by a lognormal, by (1 - C). Pleural mesothelioma is a special case when C = 0.

Adult↗
PubMed1997

Mapdiff: determining differences between two genomic maps.

MOTIVATION: When inspecting two maps of a chromosome or chromosomal region derived by similar or different methodologies, a computer-generated description of their differences is valuable, both to guide laboratory research as well as to assist version control. Our program, Mapdiff, can be used to compare two independently derived maps, or two revisions of the same map. Its usefulness increases in proportion to the percentage of shared objects between the two maps. Mapdiff uses a greedy algorithm to determine differences between shared objects. RESULTS: We illustrate Mapdiff's use in comparing the publicly available STS-content and radiation hybrid maps of human chromosome 12. AVAILABILITY: Freely available, (source, executables for Windows/DOS and Sun Solaris, documentation) on request from the author.

Algorithms↗
PubMed2000

Building a large-scale perioperative anaesthesia outcome-tracking database: methodology, implementation, and experiences from one provider within the German quality project.

The German Society of Anaesthesiology and Intensive Care Medicine evaluates voluntary, standardized, everyday, perioperative anaesthesia outcome measures. A standard minimal data set is collected for national benchmarking. This article reviews the implementation of a data acquisition system in one academic centre that has participated in this long-term nationwide project since its initiation in 1992. The population studied comprised 96,107 patients up to 1997. The overall incidence of anaesthesia-related incidents, events and complications (IEC) was 22%. Results are presented and discussed for 63 different IEC, seven functional system categories and five severity grades. The proposed methodology, using computer-readable records, was suitable for comprehensive and detailed outcome documentation. However, an extensive data validation system was necessary. IEC reporting results were largely dependent on the documentation culture. The future of outcome tracking in routine anaesthesia may lie in multicentre comparisons with multivariate-adjusted risk and comorbidity data from each provider's integrated information system.

Algorithms↗
PubMed2002

BEST: a novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development.

Embryonic gene expression patterns are an indispensable part of modern developmental biology. Currently, investigators must visually inspect numerous images containing embryonic expression patterns to identify spatially similar patterns for inferring potential genetic interactions. The lack of a computational approach to identify pattern similarities is an impediment to advancement in developmental biology research because of the rapidly increasing amount of available embryonic gene expression data. Therefore, we have developed computational approaches to automate the comparison of gene expression patterns contained in images of early stage Drosophila melanogaster embryos (prior to the beginning of germ-band elongation); similarities and differences in gene expression patterns in these early stages have extensive developmental effects. Here we describe a basic expression search tool (BEST) to retrieve best matching expression patterns for a given query expression pattern and a computational device for gene interaction inference using gene expression pattern images and information on the associated genotypes and probes. Analysis of a prototype collection of Drosophila gene expression pattern images is presented to demonstrate the utility of these methods in identifying biologically meaningful matches and inferring gene interactions by direct image content analysis. In particular, the use of BEST searches for gene expression patterns is akin to that of BLAST searches for finding similar sequences. These computational developmental biology methodologies are likely to make the great wealth of embryonic gene expression pattern data easily accessible and to accelerate the discovery of developmental networks.

Algorithms↗
PubMed2003

Confidence regions and hypothesis tests for topologies using generalized least squares.

A confidence region for topologies is a data-dependent set of topologies that, with high probability, can be expected to contain the true topology. Because of the connection between confidence regions and hypothesis tests, implicitly or explicitly, the construction of confidence regions for topologies is a component of many phylogenetic studies. Existing methods for constructing confidence regions, however, often give conflicting results. The Shimodaira-Hasegawa test seems too conservative, including too many topologies, whereas the other commonly used method, the Swofford-Olsen-Waddell-Hillis test, tends to give confidence regions with too few topologies. Confidence regions are constructed here based on a generalized least squares test statistic. The methodology described is computationally inexpensive and broadly applicable to maximum likelihood distances. Assuming the model used to construct the distances is correct, the coverage probabilities are correct with large numbers of sites.

Animals↗
PubMed2004

Evaluation of indoor gamma radiation dose in dwellings.

The use of materials containing naturally occurring radionuclides for house construction may enhance the natural radiation background to which some population groups are exposed. External exposure results from gamma emitter radionuclides existing in the walls, floor and ceiling. Mathematical models can be used to predict external dose rates inside a room, provided the compartment geometry and the radionuclide concentration activities are known. This paper presents a methodology and a computer code for theoretical evaluation of indoor external gamma doses in the air. The room was modelled as three pairs of rectangular slabs of finite thickness. Doses were evaluated by applying a photon transport model, taking into account self-absorption and radiation build-up. Calculations were performed for 40K, 226Ra and 232Th, considering concrete walls. The results obtained show good agreement with those reported in the literature. Dose conversion factors are presented in a practical manner, ready to use for radiological impact screening.

Air Pollution, Indoor↗
PubMed2001

Effect of dose levels on the diagnostic performance of a selenium-based digital chest system.

RATIONALE AND OBJECTIVES: To evaluate the effect of dose reduction on diagnostic performance by using a digital chest imaging system in which amorphous selenium serves as the x-ray detector. METHODS: Two hundred forty-seven patients were examined with the selenium system. Three sets of images were made in each patient: one set with a standard x-ray dose, one set with 55% of the standard dose, and one set with 35% of the standard dose. All 741 images were read by two radiologists. The diagnostic value of each set of images for detection of pulmonary, mediastinal, and pleural pathology was analyzed with receiver operating characteristic (ROC) methodology by using computed tomography as the reference standard. The authors also assessed the effect of sex, height, and weight of the patients on the diagnostic performance of the readers. RESULTS: The areas under the ROC curves for the detection of various abnormalities at 100%, 55%, and 35% of the standard dose for observer 1, respectively, were pulmonary opacities 0.82, 0.83, 0.84; interstitial disease 0.71, 0.70, 0.72; mediastinal disease 0.81, 0.80, 0.77; and pleural abnormalities 0.71, 0.72, 0.72. There were no statistically significant differences between the two observers. CONCLUSIONS: No statistically significant difference was found between the radiologists' performance in detecting abnormalities with standard x-ray dose images and the performance with images made with 55% and 35% of the standard dose. Sex, height, and weight had no influence on diagnostic performance.

Area Under Curve↗
PubMed1980

Optimal investigation policies under selected PSRO procedures.

This article presents a methodology for utilization review which aids the local Professional Standards Review Organization (PSRO) in selecting optimal timing of Concurrent Stay certification by diagnosis. This procedure is accomplished by modeling patients' admissions, inpatients stays and discharges for each diagnosis as a stochastic process which is audited under the PSRO by three utilization review techniques: preadmission, concurrent and retrospective review. The timing of concurrent stay certification is determined so that the maximum benefits are derived for the utilization review cost expanded. The methodology presented here is a tool to aid local PSRO management in determining the most cost-beneficial utilization review process to utilized in their jurisdiction. It is not an attempt to demonstrate the effectiveness of our utilization review policy over another in general. On the contrary, while the model is generalizable to every PSRO, the utilization review policies resulting from any application are situation-specific. The major contributions of this article are new insight into modeling the utilization review process and the provision of a methodology for which computer programs exist and are readily available to any PSRO that should desire to determine its utilization review procedure in this cost-benefit framework. In order to apply the model it is necessary that certain parameters specific to the application site be estimated or assumed. Exact procedures to aid the PSRO in parameter estimation is the subject of current investigation.

Concurrent Review↗
PubMed1999

Imaging developing brain infarction.

Continued advances in neuroimaging technology have made it practical to image multiple aspects of evolving brain infarction during the potential window period of therapeutic opportunity in stroke. Recent methodologic developments include computed tomography angiography and perfusion, and the description of quantitative parameters for magnetic resonance blood oxygen level-dependent perfusion imaging. In pathophysiologic studies, metabolism and function in the ischemic focus and the peri-infarct tissue have been further characterized. Clinical studies have focused on the applications of computed tomography and magnetic resonance imaging for prethrombolysis patient selection. These methods have an important role in the evaluation and development of new pharmaceutical agents and will be increasingly used in clinical practice as new therapies become available.

Brain↗
PubMed2006

Does low participation in cohort studies induce bias?

BACKGROUND: Participation rates in large cohort studies have decreased during the last 2 decades. The consequences of this trend for relative risk estimation are unknown. METHODS: The impact of a low participation rate (30%) on the Danish National Birth Cohort was examined among 49,751 women from the source population, including 15,373 participants in the cohort study. On the basis of independent data collection, we estimated odds ratios (ORs) in the source population and among participants for 3 exposure-risk associations: (a) in vitro fertilization and preterm birth, (b) smoking during pregnancy and birth of a small-for-gestational-age infant, and (c) prepregnancy body mass index and antepartum stillbirth. The effect of nonparticipation was described by a relative odds ratio (ROR), calculated as the OR(participants)/OR(source population). Two methods for calculation of confidence intervals for the relative odds ratio also were assessed. RESULTS: The effect of nonparticipation on the selected ORs was small. The relative ORs were close to one and the bias was never larger than 16%, although some of the confidence intervals were wide. The 2 methods for calculation of confidence intervals gave very similar results and a small simulation study showed that the coverage probabilities were close to the 95% nominal level. CONCLUSION: For the 3 chosen associations, the ORs were not biased by nonparticipation. The results are reassuring for studies based on the Danish cohort and similar cohorts of pregnant women. The methodology used to compute confidence intervals for the relative odds ratios performed well in the scenarios considered.

Adult↗
PubMed1990

Circumferential quantitative analysis of planar 201T1 myocardial scintigraphy in the diagnosis of coronary artery disease.

Methodology for the computer analysis of 201T1 myocardial perfusion images has been developed by several laboratories. Substantial evidence of the advantage of this approach over visual inspection alone has been reported. The currently available computer analyses use different algorithms to analyze 201T1 kinetics in the myocardium. The authors evaluated and compared two widely used software programs, Medical Data System (MDS): a mean-count profile, and the Cedars Sinai (CS): a maximal-count profile, of planar 201T1 scintigraphy for their ability to detect coronary artery disease (CAD).

Adult↗
PubMed2002

System approach to modeling metabolite formation from parent drug: a working example with methotrexate.

The aim of this methodological study was to present and exemplify a system-approach-based technology in modeling the formation of the metabolite from the parent drug. To represent this process, the parent-metabolite dynamic system was defined in such a way that the concentration-time profile of the parent drug was considered the input, while the concentration-time profile of the metabolite the output, of this system. The system-approach-based modeling technology was used to determine the model of the parent-metabolite dynamic system and to obtain the model-based estimates of the rate of metabolite formation, the rate of metabolic ratio and the mean time of metabolite formation. The technology was applied to concentration data for methotrexate and 7-hydroxymethotrexate in patients with psoriasis after a single oral methotrexate dose. Third-order linear models were selected as optimal to approximate the parent-metabolite dynamic systems representing the formation of 7-hydroxymethotrexate from methotrexate of these patients. The model-based estimates of the metabolic ratios ranged from 0.53 to 0.95. The model-based estimates of the mean times of formation of 7-hydroxymethotrexate from methotrexate ranged from 9.13 to 25.13 h. The model-based estimates of the rates of formation of 7-hydroxymethotrexate from methotrexate reached peak values (ranging from 0.03 to 0.11 h-1) in the time interval 1.5-4.5 h after administration of methotraxate. This study does not only introduce the method that may be useful in gaining insight into metabolite formation, but also presents a new example of the methodological, conceptual and computational uniformity of the system-approach-based technology in modeling various biomedical systems.

Administration, Oral↗
PubMed2004

SAS programs for real-time RT-PCR having multiple independent samples.

Relative real-time reverse transcription PCR (RT-PCR) has become an important tool for quantifying changes in messenger RNA (mRNA) populations following differential development or stimulation of tissues or cells. However, the best methods for conducting such experiments and analyzing the resultant data remain an issue of discussion. In this report we describe an appropriate experimental methodology and the computer programs necessary to generate a meaningful statistical analysis of the combined biological and experimental variability in such experiments. Specifically, logarithmic transformations of raw fluorescence data from the log-linear portion of real-time PCR growth curves for both target and reference genes are analyzed using a SAS/STAT Mixed Procedure program specifically designed to give a point estimate of the relative expression ratio of the target gene with associated 95% confidence interval. The program code is open-source and is printed in the text.

Algorithms↗
PubMed1991

Evaluation of performance-tested boars using a single-trait animal model.

Data structure designs for breeding value estimation of performance-tested boars using mixed-model methodology were compared. Computer models were based on estimates of parameters from the literature and from results of a survey of test station managers. Results were compared using accuracy (the correlation of true and estimated breeding values) and prediction error variance (PEV). The single-trait animal model included a fixed effect due to station-season, a random effect due to breeding value for ADG or backfat, and a random error term. Family size, number of families per test, and relationships among animals within and across tests were varied. Prediction error variance decreased faster for small families than for large ones as number of families increased, but increasing numbers of animals per pen was most important, especially if test size was optimized. With no other genetic ties, full-sibs were much more accurately evaluated than half-sibs. Designs that included sire ties among families within a station-season resulted in increased PEV. Increasing the number of full-sibs and(or) increasing the number of families per test would help to optimize PEV and correct this problem. Tying station-seasons with the relationship matrix improved the average accuracy of predicted breeding values. Placing full-sibs in different stations resulted in the greatest accuracy of evaluation, but a large number of half-sib (sire) ties resulted in comparable accuracies. Half-cousin ties did not improve accuracy of evaluation but could result in significant genetic progress by increasing the selection differential.

Adipose Tissue↗
PubMed1986

A population dynamics simulation model with application to health planning.

Despite the increasing emphasis on computers and quantitative methods in health services programs, health services administration students are denied access to many of the most powerful tools of systems analysis, including discrete event simulation, because they lack the necessary background in computer programming, simulation methodology, and stochastic processes. This article presents an approach to the modeling of the growth and decline of population groups and their attributes that can be used by students who do not have the extensive quantitative background required to develop the usual discrete event simulation models. The underlying theory, which is based on the behavior of the expectation process of vector Galton-Watson branching processes, can be explained quite easily. An example is presented that uses an age and sex specific model of population growth to investigate policy questions related to the feasibility of the construction of a long-term care facility for a defined population group. Planning decisions are based on the growth and decline of the numbers of individuals in the various age and sex groups. Extensions of the basic methodology are possible that would include projections of the variance-covariance matrix of the population sizes for each year of the projection process. In addition, the model can be extended to include projections of the impact of infectious and communicable diseases on a defined population group together with the effect of categorical disease screening and control programs. Given the basic data utilized in the model, the implementation of the calculations required by the model can be made on modern microcomputer hardware using any of the standard spreadsheet programs.

Health Planning↗
PubMed1988

How profitable is a medical career?

To assess correctly the economic profitability of any career, it is insufficient to focus only on the income earned in practicing that career. Rather, one must also account for any costs of training and for the income that is fore-gone by not pursuing the next best alternative career; in other words, earnings must be compared to their opportunity cost. When this type of analysis is applied to a medical career, it is evident that the return to physician training has declined substantially over the last 10 years. This paper discusses the methodology for correctly computing the return to a career in medicine and suggests some reasons why that return has fallen in recent years.

Data Collection↗
PubMed1999

Model based classification of cardiovascular response patterns.

A comprehensive analysis of cardiovascular control (CVC) patterns with multiple subjects is presented. It became feasible by recent methodological advances. Simple computer models were generated automatically, reproducing only factors of the true model that are relevant to the focus if investigation. These models--named aspect-models--could in turn be used in model individualization, thus reducing the necessary computational amount. The achieved speedup by a factor of more than three thousand and the high numerical stability of the resulting method allows the unsupervised identification of a large body of experimental data. The analysis of tilt table experiments of 18 subjects revealed a remarkable variety of reaction patterns. Closer examination yielded different classes of subjects. Two main groups corresponding to basic types of CVC were observed. Three outliers could be assigned to the specific situation of some subjects.

Adult↗
PubMed2000

The role of low cost communications in health in the redevelopment of the indigenous physician workforce among selected jurisdictions of the US-associated Pacific Islands.

Low cost communications in health are key to the strategic redevelopment of the indigenous physician workforce among select countries of the U.S-Associated Pacific Islands. In conducting the Pacific Basin Medical Officers Training Program (PBMOTP) from 1986-1996, the University of Hawaii established five key strategic objectives to train and support physician graduates from the Freely Associated States of the Federated States of Micronesia and the Republics of the Marshall Islands and Palau. These objectives were to: conduct a basic medical education program which graduated 70 physicians; promote regional internship training programs; assist in establishing formal postgraduate training opportunities; reestablish a regional physician's professional organization; and promote both regional and local continuing medical education activities. Inherent in the PBMOTP training program was familiarising students with hands on research methodologies, use of computers and information systems, and the processes of "store and forward" distant medical consulting. This paper documents the regional development of expanded access to medical information and distance medical communications technology and processes, including CD_Rom, Epiinfo, Picasso phone, E-mail, and Website based consult and Medical information search. Recently, email and Internet processes have promoted access to and the use of low cost communications in health thereby further reducing professional isolation among the new physician workforce in Micronesia.

Career Choice↗