SEARCH · PubMed Health

Results for “Measuring algorithm”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 307 records · Page 17Linked to original sources

PubMed2003

Diffusion and partition of solutes in cartilage under static load.

We describe experimental apparatus, methodology and mathematical algorithms to measure diffusion and partition for typical small ionic solutes and inulin (a medium size solute) in statically loaded cartilage. The partition coefficient based on tissue water (K(H(2)O)) of Na(+) increased from 1.8 to 4.5 and for SO(4)(-2) decreased from 0.5 to 0.1, when the applied pressure was raised from zero to 22 atm K(H(2)O) of inulin decreased from 0.3 to 0.05, for an increase in pressure from zero to 11 atm. Our theoretical interpretation of the results is that the partition coefficient can be expressed as a function of fixed charge density (FCD) for both loaded and unloaded cartilage. The partition coefficient shows good agreement with the ideal Gibbs-Donnan equilibrium, particularly when FCD is based on extrafibrillar water (EFW). The diffusion coefficients, D also decreased with an increase in applied pressure; raising the pressure from 0 to 22 atm resulted in the following changes in the values of D: for Na(+) from 2.86 x 10(-6) to 1.51 x 10(-6) cm(2)/s, for SO(4)(-2) from 1.58 x 10(-6) to 7.5 x 10(-7) cm(2)/s, for leucine from 1.69 x 10(-6) to 8.30 x 10(-7) cm(2)/s and for inulin from 1.80 x 10(-7) to 3.30 x 10(-8) cm(2)/s. For the three small solutes (two charged and one neutral) the diffusion coefficient D is highly correlated with the fraction of fluid volume in the tissue. These experimental results show good agreement with the simple model of Mackie and Meares: hence solute charge does not affect the diffusion of small solutes under load. For inulin D & K show some agreement with a modified Ogston model based on two major components, viz., glycosaminoglycans (GAG) and core protein. We conclude that the changes in the partition and diffusion coefficients of small and medium size solutes in statically loaded cartilage can be interpreted as being due to the reduction in hydration and increase in FCD. The change in the latter affects the partition of small ionic solutes and the partition and diffusion of larger molecules. Our results throw light on the ionic environment of chondrocytes in loaded cartilage as well as on the transport of solutes through the matrix.

Adult↗

PubMed1999

Evaluation of a workplace hemochromatosis screening program.

Hemochromatosis is a common inherited disorder of iron metabolism with significant health consequences for the employed population. Although screening for hemochromatosis has been recommended, workplace screening programs remain uncommon. In the first year of a newly initiated corporate screening program, 1968 employees were tested. The screening algorithm included measurement of serum iron and transferrin and subsequent ferritin levels in those employees with elevated iron/transferrin ratios. Thirteen percent of men and 21% of women had elevated iron/transferrin ratios. Of these, 14 men and 2 women had elevated ferritin levels. Of these 16, three had liver biopsies and all three have hemochromatosis. The cost of the screening program was $27,850. The cost per diagnosis was $9283 and the cost per year of life saved was $928. These costs compare very favorably with other common workplace screening programs. Several barriers to obtaining definitive diagnoses on all patients with a positive screening result were identified; strategies to overcome these barriers would further enhance the cost effectiveness of the program. We conclude that workplace hemochromatosis screening is highly cost effective and should be incorporated into health promotion/disease prevention programs.

Adult↗

PubMed2004

Assessment methodologies and statistical issues for computer-aided diagnosis of lung nodules in computed tomography: contemporary research topics relevant to the lung image database consortium.

Cancer of the lung and bronchus is the leading fatal malignancy in the United States. Five-year survival is low, but treatment of early stage disease considerably improves chances of survival. Advances in multidetector-row computed tomography technology provide detection of smaller lung nodules and offer a potentially effective screening tool. The large number of images per exam, however, requires considerable radiologist time for interpretation and is an impediment to clinical throughput. Thus, computer-aided diagnosis (CAD) methods are needed to assist radiologists with their decision making. To promote the development of CAD methods, the National Cancer Institute formed the Lung Image Database Consortium (LIDC). The LIDC is charged with developing the consensus and standards necessary to create an image database of multidetector-row computed tomography lung images as a resource for CAD researchers. To develop such a prospective database, its potential uses must be anticipated. The ultimate applications will influence the information that must be included along with the images, the relevant measures of algorithm performance, and the number of required images. In this article we outline assessment methodologies and statistical issues as they relate to several potential uses of the LIDC database. We review methods for performance assessment and discuss issues of defining "truth" as well as the complications that arise when truth information is not available. We also discuss issues about sizing and populating a database.

Algorithms↗

PubMed1995

The ABA-1 allergen of the parasitic nematode Ascaris suum: fatty acid and retinoid binding function and structural characterization.

We report here on the structure and function of the ABA-1 allergen protein of the parasitic nematode Ascaris, the first nematode allergen to be characterized in detail. Using the fluorescent fatty acid analog 11-(((5-(dimethylamino)-1-naphthalenyl)sulfonyl)amino)undecanoic acid (DAUDA), it was demonstrated that ABA-1 is a fatty acid binding protein (FABP) with a high affinity for the fluorescent analog (8.8 x 10(-8) M) and for oleic acid in competition experiments (1.3 x 10(-8) M), with a single binding site for ligand per monomer unit. Blue-shifting of fluorescence emission of DAUDA upon binding was unprecedented in degree among FABPs, being equivalent to that occurring in cyclohexane. A similarly blue-shifted spectrum was obtained with a probe in which the fluorophore was bound to the alpha carbon of a fatty acid, indicating that the carboxylate group of bound fatty acids is probably not exposed to solvent. In competition experiments and by observation of changes in their intrinsic fluorescence, retinol and retinoic acid were also found to bind in the fatty acid binding site. Circular dichroism (CD) of the ABA-1 protein revealed a high alpha-helix content (59%) which was consistent with the four-helix structure for the protein predicted from sequence algorithms. Fluorescence measurements showed that the single, highly conserved tryptophan residue is deeply buried in an unusually apolar environment and that this was unaffected by ligand binding. DSC studies of thermal stability indicate that unfolding of the ABA-1 dimer is cooperative and biphasic (Tm approximately 71 and 89 degrees C), suggesting a two-domain thermal unfolding process, again consistent with the predicted structure. Only the folding of the high-temperature domain is reversible on cooling. DSC confirmed the gel filtration analysis, which indicated that ABA-1 forms a dimer. Aside from being the first nematode allergen for which structure or function has been elucidated, ABA-1 provides a highly manipulable model for investigation of the interaction between hydrophobic ligands and alpha-helical proteins.

Allergens↗

PubMed2006

Structural characterization of alpha-zein.

A variety of published physical measurements, computational algorithms, and structural modeling methods have been used to create a molecular model of 19 kDa alpha-zein (Z19). Zetaeins are water-insoluble storage proteins found in corn protein bodies. Analyses of the protein sequence using probability algorithms, structural studies by circular dichroism, infrared spectroscopy, small-angle X-ray scattering (SAXS), light scattering, proton exchange, NMR, and optical rotatory dispersion experiments suggest that Z19 has approximately 35-60% helical character, made up of nine helical segments of about 20 amino acids with glutamine-rich "turns" or "loops". SAXS and light-scattering experiments suggest that in alcohol/water mixtures alpha-zein exists as an oblong structure with an axial ratio of approximately 6:1. Furthermore, ultracentifugation, birefringence, dielectric, and viscosity studies indicate that alpha-zein behaves as an asymmetric particle with an axial ratio of from 7:1 to 28:1. Published models of alpha-zein to date have not been consistent with the experimental data, and for this reason the structure was re-examined using molecular mechanics and dynamics simulations creating a new three-dimensional (3D) structure for Z19. From the amino acid sequence and probability algorithms this analysis suggested that alpha-zein has coiled-coil tendencies resulting in alpha-helices with about four residues per turn in the central helical sections with the nonpolar residue side chains forming a hydrophobic face inside a triple superhelix. The nine helical segments of the 19 kDa protein were modeled into three sets of three interacting coiled-coil helices with segments positioned end to end. The resulting structure lengthens with the addition of the N- and C-terminal sections, to give an axial ratio of approximately 6 or 7:1 in agreement with recent experiments. The natural carotenoid, lutein, is found to fit into the core of the triple-helical segments and help stabilize the configuration. Molecular dynamics simulations with explicit methanol/water molecules as solvent have been carried out to refine the 3D structure.

Models, Molecular↗

PubMed1995

Measurement of rapid release kinetics for drug delivery.

A fluorescence measurement system and methods of data analysis were developed to measure rapid kinetics of transdermal transport in vitro. Three variations on the technique were demonstrated, where the receptor compartment concentration was determined by: 1) fluorescence measurements of aliquots removed at discrete time points, 2) continuous fluorescence measurements made directly in the receptor compartment using a custom-made fluorimeter cuvette as a permeation chamber, and 3) continuous fluorescence measurements made in a flow-through cuvette containing receptor solution continuously pumped from a flow-through permeation chamber. In each case, the measured signal was a convolution of the time-dependent molecular flux (the desired information) and the characteristic response of the measurement system. Algorithms for deconvolution of the signal were derived theoretically. For the most complicated case, (3), the experimental confirmation is shown here, proving a time resolution on the order of half a minute.

Animals↗

PubMed2004

Linear scaling computation of the Fock matrix. VII. Parallel computation of the Coulomb matrix.

We present parallelization of a quantum-chemical tree-code for linear scaling computation of the Coulomb matrix. Equal time partition is used to load balance computation of the Coulomb matrix. Equal time partition is a measurement based algorithm for domain decomposition that exploits small variation of the density between self-consistent-field cycles to achieve load balance. Efficiency of the equal time partition is illustrated by several tests involving both finite and periodic systems. It is found that equal time partition is able to deliver 91%-98% efficiency with 128 processors in the most time consuming part of the Coulomb matrix calculation. The current parallel quantum chemical tree code is able to deliver 63%-81% overall efficiency on 128 processors with fine grained parallelism (less than two heavy atoms per processor).

Journal Article↗

PubMed2000

Strong Lensing Reconstruction.

We present a general linear algorithm for measuring the surface mass density 1-kappa from the observable reduced shear g=gamma&solm0;&parl0;1-kappa&parr0; in the strong lensing regime. We show that in general, the observed polarization field can be decomposed into "electric" and "magnetic" components, which have independent and redundant solutions, but orthogonal noise properties. By combining these solutions, one can increase the signal-to-noise ratio by 2. The solutions allow dynamic optimization of signal and noise, both in real and Fourier space (using arbitrary smoothing windows). Boundary conditions have no effect on the reconstructions, apart from its effect on the signal-to-noise ratio. Many existing reconstruction techniques are recovered as special cases of this framework. The magnetic solution has the added benefit of yielding the global and local parity of the reconstruction in a single step.

Journal Article↗

PubMed2005

Optical tomography of the breast using a multi-channel time-resolved imager.

A time-resolved optical tomography system has been used to generate cross-sectional images of the human breast. Images are reconstructed using an iterative, nonlinear algorithm and measurements of mean photon flight time relative to those acquired on a homogeneous reference phantom. Thirty-eight studies have been performed on three healthy volunteers and 21 patients with a variety of breast lesions including cancer. We have successfully detected 17 out of 19 lesions, and shown that optical images of the healthy breast of the same volunteer display a heterogeneity which is repeatable over a period of months. However, results also indicate that the lack of accurate quantitation of optical parameters and limited morphological information limits the ability to characterize different types of lesions and distinguish benign from malignant tissues. Drawbacks of our current methodology and plans for overcoming them are discussed.

Adult↗

PubMed1987

Some physical results from an impedance camera.

We discuss some physical results from an impedance camera. We placed agar blocks of various resistivities and sizes in saline. We showed that when the agar block was small or close in resistivity to the saline solution, we were unable to reconstruct it. We attempted to reconstruct an image of a fist, but were unable to achieve this due to current flowing in the arm. We concluded that three-dimensional analysis may be needed, along with more sensitive reconstruction algorithms and measurements.

Agar↗

PubMed2004

An oncologist-based model of cancer genetic counselling for hereditary breast and ovarian cancer.

BACKGROUND: We describe a multistep model of cancer genetic counselling designed to promote awareness, and disease surveillance and preventive measures for hereditary and familial breast and ovarian cancer. PATIENTS AND METHODS: Step T0 of the model entails information giving; this is followed by pedigree analysis and risk estimation (T1), risk communication and genetic testing (T2), and genetic test result communication (T3). User consent was required to proceed from one step to the next. Surveillance and preventive measures are proposed to at-risk users. Of the 311 subjects who requested cancer genetic counselling, consent data to each counselling step were available for 295: 93 were disease-free, 187 had breast cancer, 12 had ovarian cancer and three had breast plus ovarian cancer. RESULTS: Consent was high at T0 (98.39%), T1 (96.40%) and T2 (99.65%). Consent decreased at the crucial points of counselling: T2 (87.71%) and T3 [genetic test result communication (85.08%), and extension of counselling to and testing of relatives (65.36%)]. CONCLUSIONS: The model fosters the user's knowledge about cancer and favours identification of at-risk subjects. Furthermore, by promoting awareness about genetic testing and surveillance measures, the algorithm enables users to make a fully informed choice of action in case of predisposing or familial cancer risk.

Breast Neoplasms↗

PubMed1996

Host-pathogen systems in a spatially patchy environment.

A discrete model for a host-pathogen system is developed and is used to represent the dynamics in each patch within a landscape of n x n patches. These patches are linked by between-generation dispersal to neighbouring patches. Important results (compared to similar 'coupled map lattice' studies) include an increase in the likelihood of metapopulation extinction if the natural loss of pathogen particles is low, and the observation of a radial wave pattern (not previously reported) where the wavefront propagates uniformly from a central focus. This result has additional significance in that it permits the system to exhibit 'intermittency' between two quasi-stable spatial patterns: spirals and radial waves. With intermittent behaviour, the dynamics may look consistent when viewed at one time scale, but over a longer time scale they can alter dramatically and repeatedly between the two patterns. There is also evidence of clear links between spatial structure and temporal metapopulation behaviour in both the intermittent and 'pure' regions, verified by results from an algorithmic complexity measure and a spectral analysis of the temporal dynamics.

Animals↗

PubMed2001

Accessing the dynamics of large many-particle systems using the stochastic series expansion.

The stochastic series expansion (SSE) method is a quantum Monte Carlo (QMC) technique working directly in the imaginary time continuum and thus avoiding "Trotter discretization" errors. Using a nonlocal "operator-loop update," it allows one to treat large quantum mechanical systems of many thousand sites. In this paper we first give a comprehensive review on SSE and present benchmark calculations of SSE scaling behavior with system size and inverse temperature, and compare it to the loop algorithm, whose scaling is known to be one of the best of all QMC methods. Finally we introduce an efficient algorithm to measure Green's functions and thus dynamical properties within SSE.

Journal Article↗

PubMed1993

Uniqueness and the ab initio phase problem in macromolecular crystallography.

The crystallographic phase problem is indeterminate in the absence of additional chemical information. A successful ab initio approach to the macromolecular phase problem must employ sufficient chemical constraints to limit the solutions to a manageably small number. Here we show that commonly employed chemical constraints - positivity, atomicity and a solvent boundary - leave the phase problem greatly underdetermined for Fourier data sets of moderate (2.5-3.0 A) resolution. Entropy maximization is also beset by multiple false solutions: electron-density maps are readily generated which satisfy the same Fourier amplitude constraints but have higher entropies than the true solution. We conclude that a successful ab initio approach must make use of high-resolution Fourier data and/or stronger chemical constraints. One such constraint is the connectivity of the macromolecule. We describe a rapid algorithm for measuring the connectivity of a map, and show its utility in reducing the multiplicity of solutions to the phase problem.

Journal Article↗

PubMed2004

Summary of the recommendations on sexual dysfunctions in men.

INTRODUCTION: There are few published guidelines for the management of sexual dysfunctions in men and women, despite the prevalence and lack of attention to these problems. Disorders of sexual function in men include erectile dysfunction, orgasm/ejaculation disorders, priapism, and Peyronie's disease. AIM: To provide evidence-based and expert-opinion consensus guidelines for the clinical management of men's sexual dysfunctions. METHODS: An International Consultation in collaboration with major urological and sexual medicine societies assembled over 200 multidisciplinary experts from 60 countries into 17 consultation committees. Committee members established the scope and objectives for each chapter. Following intensive review of available data and publications, committees developed evidence-based guidelines in each area. MAIN OUTCOME MEASURE: New algorithms and guidelines for assessment and treatment of men's sexual dysfunction were developed. The Oxford system of evidence-based review was systematically applied. Expert opinion was based on systematic grading of the medical literature, in addition to cultural and ethical considerations. RESULTS: Recommendations and guidelines for men's sexual dysfunction are presented. These guidelines were developed as evidence-based, patient-centered, and multidisciplinary in focus. For the clinical assessment and diagnosis of ED, a basic evaluation was recommended for all patients, with optional and specialized testing reserved for special cases. A new treatment algorithm is proposed. This algorithm provides a clinically relevant guideline for managing ED in the large majority of men. New treatment guidelines and algorithms are provided for men's orgasm and ejaculation disorders, including premature ejaculation, retrograde and delayed ejaculation. Finally, expert opinion-based guidelines for the clinical management of priapism and Peyronie's disease are provided. CONCLUSIONS: Additional research is needed to validate and extend these guidelines. Nonetheless, this summary encompasses the recommendations concerning men's sexual dysfunctions presented at the 2nd International Consultation on Sexual Medicine in Paris, France, June 28-July 1, 2003.

Algorithms↗

PubMed2003

Effectiveness of compensating filters in the presence of tissue inhomogeneities.

CT based 3D treatment planning systems (3DTPS) can be used to design compensating filters that, in addition to missing tissue compensation, can account for tissue inhomogeneities. The use of computer-driven systems provides a practical, convenient, and accurate method of fabricating compensating filters. In this work, we have evaluated a commercially available PAR Scientific DIGIMILL milling machine linked with FOCUS 3DTPS. Compensating filters were fabricated using refined gypsum material with no additives. Thus, filters were of manageable dimensions and were not sensitive to common machining errors. Compensating filters were evaluated using a homogeneous step phantom and step phantoms containing various internal inhomogeneities (air, cork, and bone). The accuracy of two planning algorithms used to design filters was experimentally evaluated. The superposition algorithm was found to produce better agreement with measurements than the Clarkson algorithm. Phantom measurements have demonstrated that compensating filters were able to produce a uniform dose distribution along the compensation plane in the presence of tissue inhomogeneity. However, the dose variation was greatly amplified in planes located beyond the inhomogeneity when a single compensated beam was used. The use of parallel-opposed compensated beams eliminated this problem. Both lateral and depth-dose uniformity was achieved throughout the target volume.

Biophysics↗

PubMed2002

Developing an anatomical model of the human laryngeal cartilages from magnetic resonance imaging.

The purpose of this work was to construct a three-dimensional anatomical framework of the cartilages of the human larynx. The framework included representative surface models of the four laryngeal cartilages and estimated attachment points for the intrinsic laryngeal muscles. High-resolution magnetic resonance imaging (MRI) was used to scan one female and four male human cadaveric larynges. The cartilages were segmented manually from the MRI volume for analysis. Two of these larynges were subsequently dissected and the landmark distances on the cartilages measured for comparison with the MRI measures and previous studies. The MRI measures were 8% smaller than the anatomical measures and 12% smaller than data reported in the literature. A laryngeal coordinate system was defined using the plane of symmetry of the cricoid cartilage. Measures of cricoid cartilage symmetry had less than 3% difference between the two sides for a series of measures. An algorithm for registering larynges that minimized the root-mean-square distance between the surface of a reference cricoid cartilage and the surfaces of nonisotropically scaled candidate cricoid cartilages was evaluated. This study provided an anatomical framework for registering different larynges to the same coordinate space.

Aged↗

PubMed1988

Bone mineral measurement: automated determination of midvertebral CT section.

The selection of the computed tomographic (CT) section can introduce errors in reproducibility of several percent for bone mineral measurements. An algorithm for automated determination of the midvertebral CT section from survey radiographs was developed; it is based on ridge-line tracking of the vertebral end plates. The midvertebral section is defined by all points with equal perpendicular distance to the regression lines fitted through these end-plate contours. The algorithm can be corrected by manual interaction in case of failure. It was tested on T-12 to L-4 vertebrae on 25 randomly selected localizer radiographs. Of the 250 endplate contours, 223 (89.2%) were tracked automatically; the remaining 27 (10.8%) required user interaction for successful completion.

Algorithms↗