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PubMed1991

Legal methodology as nursing problem solving.

This article presents legal methodology as a form of nursing research. The four elements of the legal methodology are examined. The sources of legal authority are explained and the essential components of one case, Sermchief v Gonzales are presented in detail as an illustration of the legal methodology. In addition to the elements of the methodology, the methodological tools for the process are described. The computer and manual searching strategies are identified. Finally, the citation system which serves as an integral portion of the methodological process is discussed.

Humans↗
PubMed1987

Computer-aided design of a prosthetic socket for an above-knee amputee.

A computer-aided design process for fabricating the rectified cast for an above-knee prosthetic socket is described. The methodology for collecting the parameters required for the computer analysis is discussed. The input variables include the unloaded shape of the residual limb, the mechanical properties of the soft tissues that comprise the limb, and the surface loading that deforms the tissue. The technologies that have been developed to ascertain these parameters are presented, and the clinical experience of using the computer-generated shape is presented.

Artificial Limbs↗
PubMedDate not supplied

The General Practice Morbidity Database Project Wales--a methodology for primary care data extraction.

There is a fundamental need for accurate, timely and relevant information for health service planning; the increasing focus on a primary care led NHS has made the collection of information from general practitioners a priority. A collaborative project between general practitioners and public health physicians in Wales has developed methodologies for the extraction and analysis of routinely collected data from general practices across Wales. Four commonly used computer systems have been investigated. This paper outlines the methodologies used and describes the problems encountered and their solutions.

Computer Communication Networks↗
PubMed2004

Ultrasound-guided lumbar facet nerve block: accuracy of a new technique confirmed by computed tomography.

BACKGROUND: Lumbar facet nerve (medial branch) blocks are often used to diagnose facet joint-mediated pain. The authors recently described a new ultrasound-guided methodology. The current study determines its accuracy using computed tomography scan controls. METHODS: Fifty bilateral ultrasound-guided approaches to the lumbar facet nerves were performed in five embalmed cadavers. The target point was the groove at the cephalad margin of the transverse (or costal) process L1-L5 (medial branch T12-L4) adjacent to the superior articular process. Axial transverse computed tomography scans, with and without 1 ml contrast dye, followed to evaluate needle positions and spread of contrast medium. RESULTS: Forty-five of 50 needle tips were located at the exact target point. The remaining 5 were within 5 mm of the target. In 47 of 50 cases, the applied contrast dye reached the groove where the nerve is located, corresponding to a simulated block success rate of 94% (95% confidence interval, 84-98%). Seven of 50 cases showed paraforaminal spread, 5 of 50 showed epidural spread, and 2 of 50 showed intravascular spread. Despite the aberrant distribution, all of these approaches were successful, as indicated by contrast dye at the target point. Abnormal contrast spread was equally distributed among all lumbar levels. Contrast traces along the needle channels were frequently observed. CONCLUSIONS: : The computed tomography scans confirm that our ultrasound technique for lumbar facet nerve block is highly accurate for the target at all five lumbar transverse processes (medial branches T12-L4). Aberrant contrast medium spread is comparable to that of the classic fluoroscopy-guided method.

Aged↗
PubMed1999

Tanford-Kirkwood electrostatics for protein modeling.

Solvent plays a significant role in determining the electrostatic potential energy of proteins, most notably through its favorable interactions with charged residues and its screening of electrostatic interactions. These energetic contributions are frequently ignored in computational protein design and protein modeling methodologies because they are difficult to evaluate rapidly and accurately. To address this deficiency, we report a revised form of the original Tanford-Kirkwood continuum electrostatic model [Tanford, C. & Kirkwood, J. G. (1957) J. Am. Chem. Soc. 79, 5333-5339], which accounts for the effects of solvent polarization on charged atoms in proteins. The Tanford-Kirkwood model was modified to increase its speed and to improve its sensitivity to the details of protein structure. For the 37 electrostatic self-energies of the polar side-chains in bovine pancreatic trypsin inhibitor, and their 666 interaction energies, the modified Tanford-Kirkwood potential of mean force differs from a computationally intensive numerical potential (DelPhi) by root-mean-square errors of 0.6 kcal/mol and 0.08 kcal/mol, respectively. The Tanford-Kirkwood approach makes possible a realistic treatment of electrostatics in computationally demanding protein modeling calculations. For example, pH titration calculations for ovomucoid third domain that model polar side-chain relaxation (including >2 x 10(23) rotamer conformations of the protein) provide pKa values of unprecedented accuracy.

Models, Theoretical↗
PubMed2005

Molecular dynamics and protein function.

A fundamental appreciation for how biological macromolecules work requires knowledge of structure and dynamics. Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled with improvements in methodology makes this an exciting time for the application of simulation to structural biology. In this Perspective we survey two areas, protein folding and enzymatic catalysis, in which simulations have contributed to a general understanding of mechanism. We also describe results for the F(1) ATPase molecular motor and the Src family of signaling proteins as examples of applications of simulations to specific biological systems.

Animals↗
PubMed2002

Prospective prediction in the presence of missing data.

A variety of methods and algorithms are available for estimating parameters in the class of a generalized linear model in the presence of missing values. However, there is little information on how this already built model can be used for prediction in new observations with missing data in the covariates. Dropping the observations with missing values is a widespread practice with serious statistical and non-statistical implications. One solution is to fit separate regression models, or submodels, to each pattern of missing covariates. In practice, for any iterative regression method, this approach is computationally intensive. We propose a simple methodology to predict outcomes for individuals with incomplete information based on the estimated coefficients and covariance from the already built model. This method does not require revisiting the original data set used to build the original model and works by generating a first-order approximation of any submodel coefficient estimates. This is achieved by using the SWEEP operator on an augmented covariance matrix obtained from the original model. We refer to this approach as the one-step sweep (OSS) method. The methodology is demonstrated using data from the Department of Veterans Affairs Continuous Improvement in Cardiac Surgery Program (CICSP). These data contain 30 day mortality, the outcome of interest, and risk information for over 14,000 patients who underwent coronary artery bypass grafting (CABG) surgery over a four-year period. Using complete data from the first 3.5 years of this study period, a logistic regression model was built. This model was then used to predict mortality for patients undergoing CABG in the most recent 6-months. In order to evaluate the performance of the OSS method we randomly generated observations with missing covariates in the 6-month prediction database. We use this simulation to demonstrate that the computationally efficient OSS substantially reduces the error in risk-adjusted mortality created when cases with incomplete information are eliminated. Lastly, we derive the relationship between the OSS method and data imputation.

Computer Simulation↗
PubMed2004

Registration of biplane angiography and intravascular ultrasound for 3D vessel reconstruction.

UNLABELLED: If planned and applied correctly, intra-vascular brachytherapy (IVB) can significantly reduce the risk of restenosis after interventional treatment of stenotic arteries. OBJECTIVES: In order to facilitate computer-based IVB planning, a three-dimensional reconstruction of the stenotic artery based on intravascular ultrasound (IVUS) sequences is desirable. METHODS: To attain a 3D reconstruction, the frames of the IVUS sequence are properly aligned in space and completed with additional intermediate frames generated by interpolation. The alignment procedure uses additional information that is obtained from biplane X-ray angiography performed simultaneously during the capturing of the IVUS sequence. After IVUS images and biplane angiography data are acquired from the patient, the vessel-wall borders and the IVUS catheter are detected by an active contour algorithm. Next, the twist between adjacent IVUS frames is determined by a sequential triangulation method combined with stochastic analysis. RESULTS: The above procedure results in a 3D volume-model of the vessel, which also contains information from the IVUS modality. This data is sufficient for computer-based intravascular brachytherapy planning. CONCLUSION: The proposed methodology can be used to improve the current state-of-the-art IVB treatment planning by enabling computerized dosage computations on a highly accurate 3D model.

Algorithms↗
PubMed1995

Making a place for teaching about family violence in medical school.

Although family violence is a common cause of patients' problems, it has not yet received sufficient attention in medical school curricula. There are several possible reasons for this delay, including the fact that teaching about family violence is complicated because there are no "quick fix" interventions, the approaches are often complex and multidisciplinary, and there may be limited resources for response in many communities. The author offers a variety of suggestions for incorporating family violence topics in the medical school curriculum, such as: (1) expose students to information about family violence in their preclinical training, and integrate family violence issues into clinical instruction (several examples are given); (2) use problem-based teaching formats when possible, since these lend themselves well to the integration of family violence issues into case presentations; (3) enrich the curriculum by the participation of a variety of non-MD experts who deal with family violence issues, and take students out of the classroom to shelters and other relevant locations; (4) teach a prevention-oriented approach, just as is taught for the areas of smoking, seat belt use, weight control, etc.; (5) use standardized patients, interactive computer-based learning, and other innovative methodologies to help preclinical students perfect their interviewing and examination skills; (6) during the clinical years, include violence as part of the differential diagnosis of common medical complaints; (7) give attention to the education of residents for consistent teaching and reinforcement of principles learned in medical school, and integrate family violence education into the entire continuum of physicians' education; (8) build appropriate expectations into accreditation requirements and into medical licensing and specialty certifying examinations.(ABSTRACT TRUNCATED AT 250 WORDS)

Accreditation↗
PubMed1982

Computer-analysed movements in three dimensions recorded by light-emitting diodes. A study of methodological errors and of evaluation of chewing behaviour in a group of young adults.

Mandibular movements recorded by means of intraorally placed light-emitting diodes (LEDs) were described and tested. By using a reference system attached to the test subject, the influence of head movements on the registration of the mandibular movements could be avoided. The errors of the method were tested. The stability of the reference system during function was found to be greater when the light impulses did not have to penetrate the lip. A limited clinical test was performed and the following observations were made: the mean cycle duration was, after the first cycles, stable through the whole chewing phase, 0.52 s when chewing crispbread; the duration of the occlusion phase appeared to be shorter than that of the opening and closing phases; the velocity of the mandible was greater in the opening phase than in the closing phase, with a mean velocity of 84 and 70 mm/s respectively; the clinical test showed that the method was easy to handle in the clinical situation, thereby creating an instrument for studies in larger groups of patients. By adding a simple computer program, the manual analysis could be reduced considerably and a number of variables could be measured with a high degree of precision.

Adult↗
PubMed2005

SPINEVOLUTION: a powerful tool for the simulation of solid and liquid state NMR experiments.

Exact numerical simulations of NMR experiments are often required for the development of new techniques and for the extraction of structural and dynamic information from the spectra. Simulations of solid-state magic angle spinning (MAS) experiments can be particularly demanding both computationally and in terms of the programming required to carry them out, even if special simulation software is used. We recently developed a number of approaches that dramatically improve the efficiency and allow a high degree of automation of these computations. In the present paper, we describe SPINEVOLUTION, a highly optimized computer program that implements the new methodology. The algorithms used in the program will be described separately. Although particularly efficient for the simulation of experiments with complex pulse sequences and multi-spin systems in solids, SPINEVOLUTION is a versatile and easy to use tool for the simulation and optimization of virtually any NMR experiment. The performance of SPINEVOLUTION was compared with that of another recently developed NMR simulation package, SIMPSON. Benchmarked on a series of examples, SPINEVOLUTION was consistently found to be orders of magnitude faster. At the time of publication, the program is available gratis for non-commercial use.

Algorithms↗
PubMed2005

Computational steering in Monte Carlo simulations of thin film polystyrene.

High molecular weight polymer systems show very long relaxation times, of the order of milliseconds or more. This time-scale proves practically inaccessible for atomic-scale dynamical simulation such as molecular dynamics. Even with a Monte Carlo (MC) simulation, the generation of statistically independent configurations is non-trivial. Many moves have been proposed to enhance the efficiency of MC simulation of polymers. Each is described by a proposal density Q(x'; x): the probability of selecting the trial state x' given that the system is in the current state x. This proposal density must be parametrized for a particular chain length, chemistry and temperature. Choosing the correct set of parameters can greatly increase the rate at which the system explores its configuration space. Computational steering (CS) provides a new methodology for a systematic search to optimize the proposal densities for individual moves, and to combine groups of moves to greatly improve the equilibration of a model polymer system. We show that monitoring the correlation time of the system is an ideal single parameter for characterizing the efficiency of a proposal density function, and that this is best evaluated by a distributed network of replicas of the system, with the operator making decisions based on the averages generated over these replicas. We have developed an MC code for simulating an anisotropic atomistic bead model which implements the CS paradigm. We report simulations of thin film polystyrene.

Algorithms↗
PubMed2006

Direct parallel image reconstructions for spiral trajectories using GRAPPA.

The use of spiral trajectories is an efficient way to cover a desired k-space partition in magnetic resonance imaging (MRI). Compared to conventional Cartesian k-space sampling, it allows faster acquisitions and results in a slight reduction of the high gradient demand in fast dynamic scans, such as in functional MRI (fMRI). However, spiral images are more susceptible to off-resonance effects that cause blurring artifacts and distortions of the point-spread function (PSF), and thereby degrade the image quality. Since off-resonance effects scale with the readout duration, the respective artifacts can be reduced by shortening the readout trajectory. Multishot experiments represent one approach to reduce these artifacts in spiral imaging, but result in longer scan times and potentially increased flow and motion artifacts. Parallel imaging methods are another promising approach to improve image quality through an increase in the acquisition speed. However, non-Cartesian parallel image reconstructions are known to be computationally time-consuming, which is prohibitive for clinical applications. In this study a new and fast approach for parallel image reconstructions for spiral imaging based on the generalized autocalibrating partially parallel acquisitions (GRAPPA) methodology is presented. With this approach the computational burden is reduced such that it becomes comparable to that needed in accelerated Cartesian procedures. The respective spiral images with two- to eightfold acceleration clearly benefit from the advantages of parallel imaging, such as enabling parallel MRI single-shot spiral imaging with the off-resonance behavior of multishot acquisitions.

Algorithms↗
PubMed2003

Estimation of bolus dispersion effects in perfusion MRI using image-based computational fluid dynamics.

Bolus tracking magnetic resonance imaging (MRI) is a powerful technique for measuring perfusion, and is playing an increasing role in the investigation of acute stroke. However, limitations have been reported when assessing patients with steno-occlusive disease. The presence of a steno-occlusive disease in the artery may cause bolus dispersion, which has been shown to introduce significant errors in cerebral blood flow (CBF) quantification. Bolus dispersion is commonly described by a vascular transport function, but the function that properly characterizes the dispersion is unknown. A novel method to quantify bolus dispersion errors on perfusion measurements is presented. A realistic patient-specific model is constructed from anatomical and physiologic MR data, and the arterial blood flow pattern and the transport of the bolus of contrast agent are computed using finite element analysis. The methodology presented was used also to evaluate the accuracy of three simple vascular models. The methodology was tested on MR data from two normal subjects and two subjects with mild carotid artery stenosis. The estimated CBF errors were of the order of 15% to 20%. However, the presence of stenosis did not necessarily introduce larger dispersion (not only the geometrical model but also the particular physiologic conditions influence the degree of bolus dispersion). The method described will contribute to a better understanding of errors introduced by dispersion effects, to the assessment and validation of vascular models, and to the development of new methods for the correction of dispersion errors in CBF quantification.

Blood Flow Velocity↗
PubMed1994

123I-IBZM SPECT: reconstruction methodology and results in parkinsonism and dystonia.

In 58 patients with Parkinsonism or dystonia striatal dopamine D2 receptors were investigated using 123I-iodobenzamide (123I-IBZM) single-photon emission computed tomography (SPECT). The influence of SPECT reconstruction methodology on semiquantification and the clinical value of 123I-IBZM SPECT were evaluated. Delineation of the striatal uptake and striatum/frontal cortex (ST/FC) ratios were improved by the use of compensation procedures for scatter and attenuation as well as the choice of an adequate filter. Satisfactory results were achieved using a Metz prefilter with a comparatively high order number (i.e. high cut-off and low suppression of higher frequencies via roll-off). Regarding clinical diagnoses it was not possible to differentiate between advanced idiopathic Parkinson's disease (IP) and Parkinsonism of other aetiology (OP) on the basis of 123I-IBZM SPECT. But patients with IP and favourable response to L-Dopa showed significantly higher ST/FC ratios than those with fluctuating response. In patients with dystonia ST/FC ratios were significantly higher compared to patients with IP or OP.

Adult↗
PubMed2000

Creating fast finite element models from medical images.

The procedure for creating a patient-specific virtual tissue model with finite element (FE) based haptic (force) feedback varies substantially from that which is required for generating a typical volumetric model. In addition to extracting geometrical and texture map data to provide visual realism, it is necessary to obtain information for supporting a FE model. Among many differences, FE-based VR environments require a FE model with appropriate material properties assigned. The FE equation must also be processed in a manner specific to the surgical task in order to maximize deformation and haptic computation speed. We are currently developing methodologies and support software for creating patient-specific models from medical images. The steps for creating such a model are as follows: 1) obtain medical images and texture maps of tissue structures; 2) extract tissue structure contours; 3) generate a 3D mesh from the tissue structure contours; 4) alter mesh based on simulation objectives; 5) assign material properties, boundary nodes and texture maps; 6) generate a fast (or real-time) FE model; and 7) support the tissue models with task-specific tools and training aids. This paper will elaborate on the above steps with particular reference to the creation of suturing simulation software, which will also be described.

Computer Graphics↗
PubMed2006

Computational prediction of genomic functional cores specific to different microbes.

Computational and experimental attempts tried to characterize a universal core of genes representing the minimal set of functional needs for an organism. Based on the increasing number of available complete genomes, comparative genomics has concluded that the universal core contains < 50 genes. In contrast, experiments suggest a much larger set of essential genes (certainly more than several hundreds, even under the most restrictive hypotheses) that is dependent on the biological complexity and environmental specificity of the organism. Highly biased genes, which are generally also the most expressed in translationally biased organisms, tend to be over represented in the class of genes deemed to be essential for any given bacterial species. This association is far from perfect; nevertheless, it allows us to propose a new computational method to detect, to a certain extent, ubiquitous genes, nonorthologous genes, environment-specific genes, genes involved in the stress response, and genes with no identified function but highly likely to be essential for the cell. Most of these groups of genes cannot be identified with previously attempted computational and experimental approaches. The large variety of life-styles and the unusually detectable functional signals characterizing translationally biased organisms suggest using them as reference organisms to infer essentiality in other microbial species. The case of small parasitic genomes is discussed. Data issued by the analysis are compared with previous computational and experimental studies. Results are discussed both on methodological and biological grounds.

Bacillus subtilis↗
PubMed2005

The bootstrap: a technique for data-driven statistics. Using computer-intensive analyses to explore experimental data.

BACKGROUND: The concept of resampling data--more commonly referred to as bootstrapping--has been in use for more than three decades. Bootstrapping has considerable theoretical advantages when it is applied to non-Gaussian data. Most of the published literature is concerned with the mathematical aspects of the bootstrap but increasingly this technique is being utilized in medical and other fields. METHODS: I reviewed the published literature following a 1994 publication assessing the transfer of technology, including the bootstrap, to the biomedical literature. RESULTS: In the ten-year period following that 1994 paper there were 1679 published references to the technique in Medline. In that same time period the following citations were found in the four major medical journals-British Medical Journal (48), JAMA (51), Lancet (52) and the New England Journal of Medicine (45). CONTENT: I introduce the basic theory of the bootstrap, the jackknife, and permutation tests. The bootstrap is used to estimate the accuracy of an estimator such as the standard error, a confidence interval, or the bias of an estimator. The technique may be useful for analysing smallish expensive-to-collect data sets where prior information is sparse, distributional assumptions are unclear, and where further data may be difficult to acquire. Some of the elementary uses of bootstrapping are illustrated by considering the calculation of confidence intervals such as for reference ranges or for experimental data findings, hypothesis testing such as comparing experimental findings, linear regression, and correlation when studying association and prediction of variables, non-linear regression such as used in immunoassay techniques, and ROC curve processing. CONCLUSIONS: These techniques can supplement current nonparametric statistical methods and should be included, where appropriate, in the armamentarium of data processing methodologies.

Computers↗