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Results for “Measuring algorithm”

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PubMed2004

Inverse scattering algorithm for reconstructing lossy fiber Bragg gratings.

We demonstrate an inverse scattering algorithm for reconstructing the structure of lossy fiber Bragg gratings. The algorithm enables us to extract the profiles of the refractive index and the loss coefficient along the grating from the grating transmission spectrum and from the reflection spectra, measured from both sides of the grating. Such an algorithm can be used to develop novel distributed evanescent-wave fiber Bragg sensors that measure the change in both the refractive index and the attenuation coefficient of the medium surrounding the grating. The algorithm can also be used to analyze and to design fiber Bragg gratings written in fiber amplifiers. A novel method to overcome instability problems in extracting the parameters of the lossy grating is introduced. The new method also makes it possible to reduce the spectral resolution needed to accurately extract the grating parameters.

Journal Article↗

PubMed2006

Protein ranking by semi-supervised network propagation.

BACKGROUND: Biologists regularly search DNA or protein databases for sequences that share an evolutionary or functional relationship with a given query sequence. Traditional search methods, such as BLAST and PSI-BLAST, focus on detecting statistically significant pairwise sequence alignments and often miss more subtle sequence similarity. Recent work in the machine learning community has shown that exploiting the global structure of the network defined by these pairwise similarities can help detect more remote relationships than a purely local measure. METHODS: We review RankProp, a ranking algorithm that exploits the global network structure of similarity relationships among proteins in a database by performing a diffusion operation on a protein similarity network with weighted edges. The original RankProp algorithm is unsupervised. Here, we describe a semi-supervised version of the algorithm that uses labeled examples. Three possible ways of incorporating label information are considered: (i) as a validation set for model selection, (ii) to learn a new network, by choosing which transfer function to use for a given query, and (iii) to estimate edge weights, which measure the probability of inferring structural similarity. RESULTS: Benchmarked on a human-curated database of protein structures, the original RankProp algorithm provides significant improvement over local network search algorithms such as PSI-BLAST. Furthermore, we show here that labeled data can be used to learn a network without any need for estimating parameters of the transfer function, and that diffusion on this learned network produces better results than the original RankProp algorithm with a fixed network. CONCLUSION: In order to gain maximal information from a network, labeled and unlabeled data should be used to extract both local and global structure.

Algorithms↗

PubMed1995

Effects of solutes on optical properties of biological materials: models, cells, and tissues.

Perturbations of scattering background for absorbance measurements by photon diffusion techniques complicate algorithms used for determining the concentration of blood and the saturation of hemoglobin in tissues. In order to better define these perturbations, we have undertaken a study of the effect of solutes, some of physiological importance, upon the scattering of three types of model systems: a lipid vessel suspension (Intralipid), a cell suspension (Baker's yeast), and a tissue (perfused liver). A simple formula relates absorbancy change to proportional changes of the input/output separation rho and the square root of mu a and mu's in relation to a relevant model system. Thus, absorbance changes at 850 nm slopes and intercepts are measured as a function of rho; the absorption and reduced scattering coefficient, mu a and mu's, are calculated. We studied each of these cases as a function of the perturbation induced by low-molecular-weight polyhydroxy solutes, generally sugars (mannitol, fructose, sucrose, and glucose), alcohols (propanediol and methanol), and electrolytes (sodium and potassium chloride). Dilatometric studies indicate volume changes of the solvent system and afford correction factors. The slopes are approximately +/- 0.5 x 10(-4) OD/mM solute per centimeter separation of input/output per percent scatter (yeast or Intralipid) and indicate possible physiological detection of solutes in tissues in the millimolar range. The large optical effects of temperature upon the solute effect on model systems and of osmotic and perfusion pressures on the perfused liver further complicate the possibility of quantitative in vivo studies of these solutes.

Animals↗

PubMed1996

Thyroid function testing based on assay of thyroid-stimulating hormone: assessing an algorithm's reliability.

OBJECTIVE: To assess the ability of an algorithm for thyroid-function testing (based on assay of thyroid-stimulating hormone [TSH]) to discern euthyroidism in patients with and without conditions affecting thyroid function. DESIGN: The Australian Health Insurance Commission (HIC) specifies clinical categories for which Medicare rebate is given for assay of both TSH and free thyroxine (FT4), but otherwise rebates for thyroid function testing are given for TSH assay only. A prospective study was made of paired TSH and FT4 results of 1000 consecutive assays categorised by indication for testing. An FT4 value within the reference range was accepted as indicating euthyroidism; the reliability of an initial TSH measurement as the sole indicator of thyroid disease was assessed against this criterion standard. SETTING: A large suburban teaching hospital. OUTCOME MEASURE: Success or failure of the algorithm, with failure defined as an abnormal FT4 level missed because the TSH level was normal. RESULTS: The algorithm failure rate both overall and in the patients not in the HIC clinical categories was 2.7%, and there was no significant difference in algorithm failure rate in the patients in the various HIC clinical categories. The categories and failure rates were: patients being monitored for thyroid disease, 3.4%; patients with the "sick euthyroid" syndrome, nil; patients with psychosis or dementia, 1.1%; patients taking drugs affecting thyroid function, 2.1%; and patients with pituitary dysfunction, one of six cases. The range of FT4 values in patients in whom the algorithm failed was 6.4-29.5 pmol/L in those without thyroid disease and 3.4-27.4 pmol/L in those with thyroid disease. In patients being monitored for thyroid disease, the proportion of abnormal values of TSH alone was significant (P<0.001). CONCLUSION: We have shown that the HIC's imposition of a TSH-based algorithm by financial fiat is also scientifically acceptable. Use of this algorithm in hospitals (including psychiatric hospitals) will result in substantial savings.

Algorithms↗

PubMed1997

A measure of DNA sequence dissimilarity based on Mahalanobis distance between frequencies of words.

A number of algorithms exist for searching genetic databases for biologically significant similarities in DNA sequences. Past research has shown that word-based search tools are computationally efficient and can find similarities or dissimilarities invisible to other algorithms like FASTA. We characterize a family of word-based dissimilarity measures that define distance between two sequences by simultaneously comparing the frequencies of all subsequences of n adjacent letters (i.e., n-words) in the two sequences. Applications to real data demonstrate that currently used word-based methods that rely on Euclidean distance can be significantly improved by using Mahalanobis distance, which accounts for both variances and covariances between frequencies of n-words. Furthermore, in those cases where Mahalanobis distance may be too difficult to compute, using standardized Euclidean distance, which only corrects for the variances of frequencies of n-words, still gives better performance than the Euclidean distance. Also, a simple way of combining distances obtained at different n-words is considered. The goal is to obtain a single measure of dissimilarity between two DNA sequences. The performance ranking of the preceding three distances still holds for their combined counterparts. All results obtained in this paper are applicable to amino acid sequences with minor modifications.

Algorithms↗

PubMedDate not supplied

An enhanced electrical impedance imaging algorithm for hyperthermia applications.

Electrical impedance imaging is a technique which is under investigation as a noninvasive method of tracking subsurface temperature distributions and/or associated cellular response during hyperthermia. In previous work, a finite element image reconstruction algorithm for converting surface potential distributions recorded at discrete electrode positions into spatial maps of conductivity values was developed. This paper reports on a series of significant improvements in the basic image reconstruction approach. Specifically, the ability to recover both the resistive and capacitive components of tissue electrical impedance have been incorporated. In addition, the image enhancement schemes of (1) total variation minimization, (2) dual meshing, and (3) spatial low-pass filtering, have been added. Through a series of simulation studies involving both phantom-like and clinically-relevant geometries having discrete regions and continuously-varying electrical property profiles, a significantly improved ability to recover spatial images of electrical properties in the impedance imaging context is demonstrated. The results show that the new algorithm is much more tolerant of measurement noise with levels up to 1% causing relatively modest degradations in image quality (compared to 0.1% which was needed previously in order to produce high quality images). The recovered electrical properties, themselves, both resistive and capacitive, are also found to be quantitative in value with errors in the 10-20% range occurring in the majority of cases, although deviations can reach 40% or more when noise levels as high as 10% are used. Temperature estimation simulations show that maximum temperature errors are significantly reduced (to approximately 2 degrees C relative to more than 10 degrees C in previous thermal simulations) with the new algorithm; however, temperature accuracies of better than 0.5 degree C on average are still found to be difficult to achieve with electrical impedance imaging even when the enhanced image reconstruction approach is used.

Algorithms↗

PubMed1996

Prevalence and identification of abnormal lipoprotein levels in a biracial population aged 23 to 35 years (the CARDIA Study). The Coronary Artery Risk Development in Young Adults Study.

This study examines the prevalence of abnormal low-density lipoprotein (LDL) and high-density lipoprotein (HDL) cholesterol levels in young adults to determine the ability of National Cholesterol Education Program Adult Treatment Panel (ATP) guidelines to identify persons with elevated LDL cholesterol, to compare other algorithms with those of the ATP, and to determine the contributions of race, gender, and other coronary artery disease risk factors to identifying patients with elevated LDL and low HDL cholesterol. The cohort was population-based, aged 23 to 35 years, and included relatively equal numbers of blacks and whites, and men and women. The prevalence of LDL cholesterol > or = 160 mg/dl (> 4.1 mmol/L) was 5% in black women, 4% in white women, 10% in black men, and 9% in white men. ATP identified most participants with elevated LDL cholesterol (range: 58.8% of white men to 70.7% of black women). Lipoprotein panels would have been required in 6% to 7% of women and to 15% to 18% of men. Algorithms that used nonlipid risk factors required more lipoprotein panels and identified fewer additional participants at risk. The prevalence of HDL cholesterol < 35 mg/dl (0.9 mmol/L) was 3% in women, 7% in black men, and 13% in white men. Algorithms that used nonlipid risk factors before measuring HDL cholesterol would require HDL cholesterol measurements in 35% of whites and 56% of blacks, but reduced sensitivity for identifying low HDL cholesterol (range: 58% in white men to 93% in black women). In young adults, algorithms based on nonlipid risk factors and family history have lower sensitivity, and increase rather than decrease the number of fasting lipoprotein panels required when compared with ATP levels.

Adult↗

PubMed1989

A reliable potentiometric measurement of ionized calcium and pH on the ICA2 Radiometer in clinical practice.

A second generation analyser for potentiometric measurement of ionized calcium and pH (ICA2 Radiometer, Copenhagen) was tested with respect to analytical performance in two different laboratories. Newly-developed aqueous buffered solutions were used at different Ca2+ concentrations as well as biological specimens prepared from human subjects. The overall precision of ICA2 was very good: CV = 0.0-0.4% for within-run and 0.4-1.7% for day-to-day precision with protein-free solutions and CV = 0.3-0.9% for within-run precision on biological specimens. The adjusted value of Ca2+ to pH 7.40 is an analytical advantage for which the calculation is correct but the assumption made for this algorithm may limit its clinical relevance. Measurements were comparable on ICA2 when performed on either whole blood, serum or plasma. Pre-analytical conditions should be observed such as the choice of anticoagulant and anaerobic conditions. Such a reliable and accurate instrument may promote the use of ionized calcium measurement in daily clinical practice.

Calcium↗

PubMedDate not supplied

Toward a velocity-resolved microvascular blood flow measure by decomposition of the laser Doppler spectrum.

Tissue microcirculation, as measured by laser Doppler flowmetry (LDF), comprises capillary, arterial, and venous blood flow. With the classical LDF approach, it has been impossible to differentiate between different vascular compartments. We suggest an alternative LDF algorithm that estimates at least three concentration measures of flowing red blood cells (RBCs), each associated with a predefined, physiologically relevant, absolute velocity in millimeters per second. As the RBC flow velocity depends on the dimension of the blood vessel, this approach might enable a microcirculatory flow differentiation. The LDF concentration estimates are derived by fitting predefined Monte Carlo simulated, single-velocity spectra to a measured, multiple-velocity LDF spectrum. Validation measurements, using both single- and double-tube flow phantoms perfused with a microsphere solution, show that it is possible to estimate velocity and concentration changes, and to differentiate between flows with different velocities. Our theory is also applied to RBC flow measurements. A Gegenbauer kernel phase function (alpha(gk)=1.05; g(gk)=0.93), with an anisotropy factor of 0.987 at 786 nm, is found suitable for modeling Doppler scattering by RBCs diluted in physiological saline. The method is developed for low concentrations of RBCs, but can in theory be extended to cover multiple Doppler scattering.

Algorithms↗

PubMed2003

Exact rotamer optimization for protein design.

Computational methods play a central role in the rational design of novel proteins. The present work describes a new hybrid exact rotamer optimization (HERO) method that builds on previous dead-end elimination algorithms to yield dramatic performance enhancements. Measured on experimentally validated physical models, these improvements make it possible to perform previously intractable designs of entire protein core, surface, or boundary regions. Computational demonstrations include a full core design of the variable domains of the light and heavy chains of catalytic antibody 48G7 FAB with 74 residues and 10(128) conformations, a full core/boundary design of the beta1 domain of protein G with 25 residues and 10(53) conformations, and a full surface design of the beta1 domain of protein G with 27 residues and 10(60) conformations. In addition, a full sequence design of the beta1 domain of protein G is used to demonstrate the strong dependence of algorithm performance on the exact form of the potential function and the fidelity of the rotamer library. These results emphasize that search algorithm performance for protein design can only be meaningfully evaluated on physical models that have been subjected to experimental scrutiny. The new algorithm greatly facilitates ongoing efforts to engineer increasingly complex protein features.

Algorithms↗

PubMed1984

Diffraction tomography using arbitrary transmitter and receiver surfaces.

The theory of diffraction tomography for two-dimensional objects within the Born approximation is presented for cases where the scattered field is measured over arbitrarily shaped boundaries surrounding the object. Reconstruction algorithms are presented for both plane wave (parallel beam) and cylindrical wave (fan beam) insonification. Special attention is devoted to cases where the measurement and source boundaries are either lines or circles. The theory and algorithms presented are shown to be readily extended to the case of three-dimensional objects.

Filtration↗

PubMed2003

Experimental validation tests of fast Fourier transform convolution and multigrid superposition algorithms for dose calculation in low-density media.

BACKGROUND AND PURPOSE: Modern conformal radiotherapy treatments require accurate dose calculation in any relevant clinical situation. One of these situations is the treatment of lung tumors, where irradiation has to be planned under challenging conditions for dose calculation. In this study we assess the errors in dose values predicted by fast Fourier transform convolution (FFTC) and multigrid superposition (MGS) algorithms implemented in a commercial treatment planning system (TPS). MATERIALS AND METHODS: FFTC and MGS algorithms were used in a FOCUS 3.0.0 (Computerized Medical Systems, USA) to calculate doses in treatment plans using photon beams of 6 and 25 MV nominal energy from a Saturne 43 linac (GE Medical Systems, USA). A 10x10-cm beam irradiating a mediastinum-lung and a thoracic wall-lung-thoracic wall modeled geometry was assessed. The calculated data were compared with measurements performed with radiographic films and ionization chamber. RESULTS: FFTC algorithm leads to an average deviation from ionometric dose measurements of over 10%. Discrepancies between measured and calculated beam fringe values (distance between 50 and 90% isodose lines) of up to 8 mm were observed. For MGS algorithm, all the points assessed in both geometries fulfilled the 3%-3 mm accuracy criteria and the average deviation of absolute dose was about 1%. A maximum of 3 mm deviation in the beam fringe for any depth was found and was within 2 mm beyond the buildup region. Deviations between ionometric and film measurements were within 3%. CONCLUSIONS: MGS algorithm assesses with reasonable accuracy dose distributions and absolute dose in inhomogeneous regions like the lung region. Therefore, and respecting the inhomogeneity dose calculation, the system could be used in routine clinical practice and in dose-escalation programs. This is not true in the case of FFTC algorithm which leads to errors greater than 10% in the absolute dose calculation and underestimates the beam fringe by up to 8 mm.

Algorithms↗

PubMed1994

The choice of approach in surgery for acoustic neuromas (vestibular schwannomas).

The advantages and disadvantages of the different surgical approaches for surgery of vestibular schwannomas are described, as well as the problems in evaluating the outcome of the treatment, regarding especially the evaluation of facial nerve function and hearing capacity. The eclectic Copenhagen treatment algorithm is outlined: 1) All tumors measuring 25 mm or more on MRI are operated via the translabyrinthine approach. 2) All patients with PTA poorer than 30 dB, and SDS poorer than 70% are operated via the translabyrinthine approach. 3) Tumors less than 10mm extrameatally, and PTA better than 30 dB and SDS better than 70% are removed via the middle fossa route. 4) Tumors measuring 10-25 mm and PTA better than 30 dB and SDS better than 70% are operated via the suboccipital route. Finally some consequences of postponing surgical treatment is described, demonstrating that 74% of 127 tumors continued to grow with a mean of 3.4 mm increased tumor diameter per year, and that 75% of patients, who were candidates for hearing preservation surgery lost the candidature in the observation period.

Algorithms↗

PubMed2000

The boundary element method in the forward and inverse problem of electrical impedance tomography.

In this paper, a new formulation of the reconstruction problem of electrical impedance tomography (EIT) is proposed. Instead of reconstructing a complete two-dimensional picture, a parameter representation of the gross anatomy is formulated, of which the optimal parameters are determined by minimizing a cost function. The two great advantages of this method are that the number of unknown parameters of the inverse problem is drastically reduced and that quantitative information of interest (e.g., lung volume) is estimated directly from the data, without image segmentation steps. The forward problem of EIT is to compute the potentials at the voltage measuring electrodes, for a given set of current injection electrodes and a given conductivity geometry. In this paper, it is proposed to use an improved boundary element method (BEM) technique to solve the forward problem, in which flat boundary elements are replaced by polygonal ones. From a comparison with the analytical solution of the concentric circle model, it appears that the use of polygonal elements greatly improves the accuracy of the BEM, without increasing the computation time. In this formulation, the inverse problem is a nonlinear parameter estimation problem with a limited number of parameters. Variants of Powell's and the simplex method are used to minimize the cost function. The applicability of this solution of the EIT problem was tested in a series of simulation studies. In these studies, EIT data were simulated using a standard conductor geometry and it was attempted to find back this geometry from random starting values. In the inverse algorithm, different current injection and voltage measurement schemes and different cost functions were compared. In a simulation study, it was demonstrated that a systematic error in the assumed lung conductivity results in a proportional error in the lung cross sectional area. It appears that our parametric formulation of the inverse problem leads to a stable minimization problem, with a high reliability, provided that the signal-to-noise ratio is about ten or higher.

Algorithms↗

PubMed1993

Seat support surface optimization using force feedback.

The development, implementation and evaluation of an algorithm designed to find optimal seat support surfaces is presented. The algorithm has been developed and implemented on an active contour measurement device. The device consists of an array of positioning elements equipped with force sensors for feedback. With a patient seated on the array, the algorithm is designed to find a seat contour that optimally satisfies given performance criteria. The performance criteria are based on measured stiffness of the soft tissues. A theoretical development of the algorithm is presented along with the modifications made to the algorithm during implementation. The results from several tests using man-made test bodies and a prototype contour gage are presented to verify the algorithm's performance.

Algorithms↗

PubMed2003

In vivo endoscopic tissue diagnostics based on spectroscopic absorption, scattering, and phase function properties.

A fast spectroscopic system for superficial and local determination of the absorption and scattering properties of tissue (480 to 950 nm) is described. The probe can be used in the working channel of an endoscope. The scattering properties include the reduced scattering coefficient and a parameter of the phase function called gamma, which depends on its first two moments. The inverse problem algorithm is based on the fit of absolute reflectance measurements to cubic B-spline functions derived from the interpolation of a set of Monte Carlo simulations. The algorithm's robustness was tested with simulations altered with various amounts of noise. The method was also assessed on tissue phantoms of known optical properties. Finally, clinical measurements performed endoscopically in vivo in the stomach of human subjects are presented. The absorption and scattering properties were found to be significantly different in the antrum and in the fundus and are correlated with histopathologic observations. The method and the instrument show promise for noninvasive tissue diagnostics of various epithelia.

Adult↗

PubMed2003

Information transmission rates of cat retinal ganglion cells.

To assess the information encoded in retinal spike trains and how it might be decoded by recipient neurons in the brain, we recorded from individual cat X and Y ganglion cells and visually stimulated them with randomly modulated patterns of various contrast and spatial configuration. For each pattern, we estimated the information rate of the cells using linear or nonlinear algorithms and for some patterns by directly measuring response probability distributions. We show that ganglion cell spike trains contain information from the receptive field center and surround, that the center and surround have similar signaling capacity, that antagonism between the mechanisms reduces information transmission, and that the total information rate is limited. We also show that a linear decoding algorithm can capture all of the information available in retinal spike trains about weak inputs, but it misses a substantial amount about strong inputs. For the strongest stimulus we used, the information rate of the best linear decoder averaged 40-70 bits/s across ganglion cell types, while the directly measured rate was around 20-40 bits/s greater. This implies that under certain stimulus conditions, visual information is encoded in the temporal structure of retinal spike trains and that a nonlinear decoding algorithm is needed to extract the temporally coded information. Using simulated spike trains, we demonstrate that much of the temporal structure may be explained by the threshold for spike generation and is not necessarily indicative of a complex coding scheme.

Algorithms↗

PubMed2006

Bipolar resistivity profiling of 3D tissue culture.

We describe a new low-cost technique for continuous monitoring of the thickness of biofilms and tissue cultures, and we demonstrate the advantage of using electrodes of different dimensions to probe different depths of a sample. We have used electric impedance spectroscopy to monitor keratinocyte stem cells (YF29) growing on an array of Ti/Pt coplanar microelectrodes. The thickness of the sample was reconstructed by fitting the measurements to theoretical curves. We have developed an algorithm for the rapid calculation of the resistance through a multilayered sample. This algorithm is based on conformal mapping and the serial partial capacitance technique. The validity of the technique was tested by measuring the sedimentation rate of an alumina powder. Sample thicknesses between 10 and 80 microm could be measured with a resolution of a few microns using the device.

Biological Assay↗