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PubMed2006

[Passive FTIR remote sensing of gaseous pollutant in heated plume].

The principle and techniques of passive remote sensing of gaseous pollutant in heated plume was illustrated and discussed in this paper. The algorithm of radiance spectra and transmittance spectra in measured region was proposed, and the method of retrieving gas concentrations with NLLS fitting algorithm was also proposed. The remote senseing of actual gaseous pollutant of smokestack was done, and the quantitative analysis of SO2 and CO2 was completed.

English Abstract↗

PubMed2003

Robust estimation of fetal heart rate variability using Doppler ultrasound.

This paper presents a new measure of heart rate variability (HRV) that can be estimated using Doppler ultrasound techniques and is robust to variations in the angle of incidence of the ultrasound beam and the measurement noise. This measure employs the multiple signal characterization (MUSIC) algorithm which is a high-resolution method for estimating the frequencies of sinusoidal signals embedded in white noise from short-duration measurements. We show that the product of the square-root of the estimated signal-to-noise ratio (SNR) and the mean-square error of the frequency estimates is independent of the noise level in the signal. Since varying angles of incidence effectively changes the input SNR, this measure of HRV is robust to the input noise as well as the angle of incidence. This paper includes the results of analyzing synthetic and real Doppler ultrasound data that demonstrates the usefulness of the new measure in HRV analysis.

Aging↗

PubMed2004

A simple and effective algorithm for detection of arbitrary Hartmann-Shack patterns.

The Hartmann-Shack sensor is well known for its capability of detecting optical aberrations from telescopic images, normally caused by the atmospheric turbulence. Since the mid-1990s, this sensor has been adapted to work with ophthalmic instrumentation to measure aberrations of the human eye. In astronomical applications, the image processing is implemented using robust closed-loop hardware systems, allowing for very high frequencies (usually in the range of 30-500 Hz). In ophthalmic instruments, this hardware solution is not proper, for two reasons: first, prices of ophthalmic instrumentation have to be at more accessible prices and, second, there is no need for ultra-high frequency closed-loop systems; in fact, as we will see along the text, recent studies of the dynamics of the eye's aberrations show that closed-loop systems of very much lower frequencies (from 10 to 40 Hz) may well eliminate the undesired micro-fluctuations in the eye's aberrations and allow for diffraction limited measurements. We have developed an effective algorithm for detection of HS patterns using an affordable commercial hardware configuration and easy to implement software. To our knowledge, this type of information has not been thoroughly disclosed elsewhere, probably due to proprietary reasons.

Algorithms↗

PubMed1999

A novel object-independent "balanced" reference scan for echo-planar imaging.

Interleaved echo-planar imaging (EPI) is susceptible to significant ghosting artifacts, resulting primarily from system time delays that cause data matrix misregistration. Most EPI applications rely on "reference scans" to measure delays, and post-processing algorithms are used to correct these errors. Unfortunately, delay estimates made with most reference scan techniques are object dependent, since they are biased by magnetic field inhomogeneities and chemical shift. The current work describes the effects of field inhomogeneities and their influence on system time delay estimation. Subsequently, a new, object-independent "balanced" reference method using two readout echo trains is proposed for time delay measurements.

Algorithms↗

PubMed2005

[Application of FTIR spectra fitting method in retrieving gas concentrations].

The method of retrieving gas concentrations by FTIR spectra measurement system is studied. NLLS fitting algorithm is used to complete the quantitative analysis of CO gas under WINDOWS operating system. The spectra of HITRAN database is employed as calibrating and training sets during the procedure of fitting FTIR spectrum. The measured IR transmittance spectra of CO are best fitted with the calculated spectra in HITRAN. The CO concentrations are acquired after the best fitting. The absolute accuracy of the results of retrieve achieves 1%-5%.

English Abstract↗

PubMed1978

Failure of total calcium corrected for protein, albumin, and pH to correctly assess free calcium status.

The clinical effectiveness of published algorithms in correcting serum total calcium (CaT) for the effects of protein, albumin, and pH was tested. Corrected calcium (CaC) values obtained by 13 of these methods were compared with values of measured free calcium (CaF) in 55 samples from normal controls and 404 samples from patients with various disorders of calcium metabolism. Three criteria were used to compare either CaC or CaT with measured CaF: 1) the correlation coefficient, 2) the average absolute deviation from measured CaF of the values of CaF predicted by the linear regression of CaF on each CaC, and 3) the number of samples in which CaC or CaT gave a different impression of normality than measured CaF. Application of the 13 published algorithms produced varied results, but none produced substantially better agreement between CaC and CaF than was found between CaT and CaF. The application of additional algorithms derived by multiple linear regression using our data base gave slightly better results than any of the published algorithms, but many values of CaC remained which were disparate from the measured value of CaF. Correction of measured total calcium by using other concurrently obtained chemistry values does not seem to adequately predict calcium status as measured by free calcium.

Autoanalysis↗

PubMed1998

AmbiPack: a systematic algorithm for packing of macromolecular structures with ambiguous distance constraints.

The determination of structures of multimers presents interesting new challenges. The structure(s) of the individual monomers must be found and the transformations to produce the packing interfaces must be described. A substantial difficulty results from ambiguities in assigning intermolecular distance measurements (from nuclear magnetic resonance, for example) to particular intermolecular interfaces in the structure. Here we present a rapid and efficient method to solve the packing and the assignment problems simultaneously given rigid monomer structures and (potentially ambiguous) intermolecular distance measurements. A promising application of this algorithm is to couple it with a monomer searching protocol such that each monomer structure consistent with intramolecular constraints can be subsequently input to the current algorithm to check whether it is consistent with (potentially ambiguous) intermolecular constraints. The algorithm AmbiPack uses a hierarchical division of the search space and the branch-and-bound algorithm to eliminate infeasible regions of the space. Local search methods are then focused on the remaining space. The algorithm generally runs faster as more constraints are included because more regions of the search space can be eliminated. This is not the case for other methods, for which additional constraints increase the complexity of the search space. The algorithm presented is guaranteed to find all solutions to a predetermined resolution. This resolution can be chosen arbitrarily to produce outputs at various level of detail. Illustrative applications are presented for the P22 tailspike protein (a trimer) and portions of beta-amyloid (an ordered aggregate).

Algorithms↗

PubMed1990

A modified algorithm of the single pool urea kinetic model.

Urea Kt/V, calculated according to the variable volume single pool urea kinetic model (UKM), has been accepted as the yardstick reflecting the adequacy of haemodialysis therapy. However, the classical algorithm of UKM requires great care in dialyser urea clearance (K) measurement in order to avoid major inaccuracies in estimating the urea distribution volume (V). Thus, we suggest a modified algorithm of UKM which avoids the measurement of K. It assumes an arbitrary V value and then calculates kinetically K as a function of the assumed V value. The rationale of the modified algorithm can be derived from the knowledge that the classical algorithm imposes a proportionality ration between K and V: given a particular set of data, a change in the attributed value of K leads to a proportional change in the calculated V value, so that the ratio K/V remains nearly constant. Aims of the study were (1) to validate the modified algorithm by comparing the resulting Kt/V and normalised protein catabolic rate (NPCR) values with the homologous ones obtained using the classical algorithm in a group of 33 patients on thrice-weekly haemodialysis; plasma water urea concentrations were used with the classical algorithm (CApw) and the modified algorithm (MApw); and (2) to verify the possibility of using plasma urea concentrations with the modified algorithm (MAp) instead of the more rigorous plasma water concentrations. NPCR (g/kg per day) was 1.33 +/- 0.05 in CApw, 1.29 +/- 0.05 in MApw and 1.28 +/- 0.04 in MAp. Kt/V was 1.27 +/- 0.03 in CApw, 1.25 +/- 0.03 in MApw and 1.26 +/- 0.03 in MAp.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗

PubMedDate not supplied

A restricted angular scattering model for electron penetration in dense media.

A restricted angular scattering model for electron penetration in dense media is presented. In the model, the Fermi-Eyges transport equation is modified through the addition of an extra term which may be interpreted as representing an apparent force opposing the scattering of electrons into wider angles. The introduction of this extra term allows the modeling of the measured saturation in the mean square angular spread of electrons with depth. The restricted scattering model retains the Gaussian features of the Fermi-Eyges model and, therefore, may be readily incorporated into existing dose computation algorithms. Good agreement is obtained with measured angular electron distribution data for a point monodirectional beam over a wide range of incident electron energies (5-20 MeV) and scattering media (atomic numbers of 6 to 82). Also, a comparison of the restricted scattering model predictions with measurements of the lateral pencil beam spread shows an improvement over the predictions of Fermi-Eyges model close to the end of the electron range. Broad beam profiles were generated using both the Fermi-Eyges and restricted scattering models. A comparison of predicted and measured beam profiles shows that the restricted scattering model is a significant improvement over the Fermi-Eyges model for the prediction of beam penumbra shape in homogeneous media.

Aluminum↗

PubMed2005

Renal advances in ultrasound elasticity imaging: measuring the compliance of arteries and kidneys in end-stage renal disease.

BACKGROUND/AIMS: Ultrasound elasticity imaging visually represents tissue hardness measurements using high-resolution ultrasound speckle-tracking algorithms. This method has recently been applied in the renal setting to measure arterial compliance in end-stage renal disease (ESRD) and the mechanical properties of transplant kidneys in vivo. METHODS: Ultrasound radio-frequency signal measurements were made of the brachial artery in 5 ESRD subjects and 5 healthy controls and renal transplant measurements in 2 subjects, 1 with chronic allograft nephropathy (CAN) and 1 with normal graft function. RESULTS: Maximal brachial artery percent strain measurements for healthy controls were 32.9 +/- 10.2% (mean +/- SD) and for ESRD subjects maximal percent strains were 4.9 +/- 1.8%. Transplant renal cortical strain for the subject with CAN was approximately one third that of the healthy transplant recipient. CONCLUSION: Ultrasound elasticity imaging offers the potential to noninvasively measure the mechanical properties of structures within the body.

Adult↗

PubMed1993

Quantifying passive resistance to motion in the straight-leg-raising test on asymptomatic subjects.

The clinician needs an objective way to measure limb motion in the straight-leg-raising test. A biomechanical algorithm was used to quantify resistance to motion in 15 asymptomatic subjects. Measurements from a pendulum electrogoniometer and hand-held load cell were used to calculate a moment representing passive resistance to motion. After three measurement trials, significant increases in range of motion (4.7%) and moment (8.4%) occurred. Then, an isometric contraction-relaxation of the hip extensors produced a highly significant increase in motion (8.8%) but decrease in moment (< 14.3%). A third order polynomial fit of moment per angle stratified the sample into two groups according to their change in moment. Motion in group 1 increased 8.0%, and in group 2, 9.5%. However, group 1 had no change in moment whereas group 2 had a highly significant decrease in moment (22.9%). The measured change in resistance demonstrated that a simple biomechanical algorithm quantified properties in a clinical test that were not observed in range of motion alone.

Adolescent↗

PubMed1996

Verification of milled two-dimensional photon compensating filters using an electronic portal imaging device.

A computer-driven milling machine is being installed at the Mallinckrodt Institute of Radiology to fabricate photon compensating filters for conventional compensation and beam-intensity modulation. Commissioning and quality assurance procedures are being developed for the design, fabrication, and delivery systems prior to using the milled filters in the clinic. The portion of the quality assurance procedures governing the filter fabrication using a computer-driven milling machine includes, in part, a comparison of designed and fabricated filters. Test filters include geometrically regular filters, such as flat surfaces and steps. The verification of these shapes is accomplished using spatial measurements. However, to test the mill's ability to generate complex curved surfaces, filters with more complicated surfaces are generated. These filters do not lend themselves to precise verification using physical measurement of the thickness distribution. A method has been developed to verify the thickness distributions of these complex filters by irradiating the filters with high-energy x rays and comparing the scattered and transmitted fluence to the fluence calculated using the intended filter shape. The fluence measurement is made using a calibrated commercial liquid ionization chamber electronic portal imaging device. The calculated fluence is separated into transmitted primary and scattered fluences and is determined using a convolution of a distributed radiation source kernel with an exponential filter attenuation function. The attenuation coefficient is measured for the filter material (Lipowitz metal) and fit to a second-order polynomial in filter thickness and off-axis distance. The distributed source kernel is measured using a split-field technique and fit to a sum of three two-dimensional Gaussian distributions. The scattered radiation is modeled by the Klein-Nishina cross section. The algorithm is tested by comparing calculated fluences with measured fluences for a series of machined filters: an open field, flat filters of 9.6-, 15.8-, and 31.6-mm thickness, split-field filters, and a pyramid-shaped filter. In each case, the algorithm calculates the fluence to within 3% of the measured values over the entire irradiated field size to within 1.5 cm of the collimated field edges.

Algorithms↗

PubMed2003

Codon adaptation index as a measure of dominating codon bias.

UNLABELLED: We propose a simple algorithm to detect dominating synonymous codon usage bias in genomes. The algorithm is based on a precise mathematical formulation of the problem that lead us to use the Codon Adaptation Index (CAI) as a 'universal' measure of codon bias. This measure has been previously employed in the specific context of translational bias. With the set of coding sequences as a sole source of biological information, the algorithm provides a reference set of genes which is highly representative of the bias. This set can be used to compute the CAI of genes of prokaryotic and eukaryotic organisms, including those whose functional annotation is not yet available. An important application concerns the detection of a reference set characterizing translational bias which is known to correlate to expression levels; in this case, the algorithm becomes a key tool to predict gene expression levels, to guide regulatory circuit reconstruction, and to compare species. The algorithm detects also leading-lagging strands bias, GC-content bias, GC3 bias, and horizontal gene transfer. The approach is validated on 12 slow-growing and fast-growing bacteria, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster. AVAILABILITY: http://www.ihes.fr/~materials.

Adaptation, Physiological↗

PubMed2001

Validation of a new algorithm for the BPM-100 electronic oscillometric office blood pressure monitor.

BACKGROUND: To test the accuracy of a new algorithm for the BPM-100, an automated oscillometric blood pressure (BP) monitor, using stored data from an independently conducted validation trial comparing the BPM-100(Beta) with a mercury sphygmomanometer. DESIGN: Raw pulse wave and cuff pressure data were stored electronically using embedded software in the BPM-100(Beta), during the validation trial. The 391 sets of measurements were separated objectively into two subsets. A subset of 136 measurements was used to develop a new algorithm to enhance the accuracy of the device when reading higher systolic pressures. The larger subset of 255 measurements (three readings for 85 subjects) was used as test data to validate the accuracy of the new algorithm. METHODS: Differences between the new algorithm BPM-100 and the reference (mean of two observers) were determined and expressed as the mean difference +/- SD, plus the percentage of measurements within 5, 10, and 15 mmHg. RESULTS: The mean difference between the BPM-100 and reference systolic BP was -0.16 +/- 5.13 mmHg, with 73.7% < or = 5 mmHg, 94.9% < or = 10 mmHg and 98.8% < or = 15 mmHg. The mean difference between the BPM-100 and reference diastolic BP was -1.41 +/- 4.67 mmHg, with 78.4% < or = 5 mmHg, 92.5% < or = 10 mmHg, and 99.2% < or = 15 mmHg. These data improve upon that of the BPM-100(Beta) and pass the AAMI standard, and 'A' grade BHS protocol. CONCLUSION: This study illustrates a new method for developing and testing a change in an algorithm for an oscillometric BP monitor utilizing collected and stored electronic data and demonstrates that the new algorithm meets the AAMI standard and BHS protocol.

Adolescent↗

PubMed2005

Tomographic fluorescence imaging in tissue phantoms: a novel reconstruction algorithm and imaging geometry.

A novel image reconstruction algorithm has been developed and demonstrated for fluorescence-enhanced frequency-domain photon migration (FDPM) tomography from measurements of area illumination with modulated excitation light and area collection of emitted fluorescence light using a gain modulated image-intensified charge-coupled device (ICCD) camera. The image reconstruction problem was formulated as a nonlinear least-squares-type simple bounds constrained optimization problem based upon the penalty/modified barrier function (PMBF) method and the coupled diffusion equations. The simple bounds constraints are included in the objective function of the PMBF method and the gradient-based truncated Newton method with trust region is used to minimize the function for the large-scale problem (39919 unknowns, 2973 measurements). Three-dimensional (3-D) images of fluorescence absorption coefficients were reconstructed using the algorithm from experimental reflectance measurements under conditions of perfect and imperfect distribution of fluorophore within a single target. To our knowledge, this is the first time that targets have been reconstructed in three-dimensions from reflectance measurements with a clinically relevant phantom.

Algorithms↗

PubMed2006

Shape-constraint region growing for delineation of hepatic metastases on contrast-enhanced computed tomograph scans.

OBJECTIVES: The objectives of this study were to develop a shape-constraint region-growing algorithm to automatically delineate liver metastases on computed tomography images and to compare automated tumor measurements with those outlined manually by radiologists. METHODS: The algorithm starts with a manual selection of a seed lesion region of interest (ROI). Based on intensity distributions of the seed ROI and the liver parenchyma, several parameters are computed and used to adaptively guide the region growing. To prevent the region growing from leaking into surrounding tissues of similar characteristics, specific shape constraints, including a local shape, a global shape, and a gravity-shift index, are developed to jointly control the iteration of the region growing. The algorithm was applied to 59 lesions in 14 patients with liver metastases. The maximal diameter (unidimension), the product of the maximal and maximal perpendicular diameters (bidimension), and the area in the axial plane were calculated for each of the segmented lesions. Three independent radiologists manually measured all the lesions once, and one of the radiologists measured each lesion 3 times. For each measurement, the concordance correlation coefficient (CCC) was used to assess the pairwise agreement between the computer and the different radiologists, and the overall concordance correlation coefficient (OCCC) was used to assess the agreement between the computer and the multiple radiologists and between the one radiologist's 3 readings. RESULTS: Fifty-three of 59 (89.8%) lesions in 14 patients with liver metastases were successfully segmented using this algorithm. The algorithm achieved a median accuracy of 88.0%. CCCs/OCCCs ranged from 0.943 to 0.999 with 95% confidence intervals. CONCLUSIONS: High accuracy and CCCs/OCCCs suggested that measurements made by the computer were very similar to those made by the radiologists.

Algorithms↗

PubMed2006

Parameter estimation in stochastic biochemical reactions.

Gene regulatory, signal transduction and metabolic networks are major areas of interest in the newly emerging field of systems biology. In living cells, stochastic dynamics play an important role; however, the kinetic parameters of biochemical reactions necessary for modelling these processes are often not accessible directly through experiments. The problem of estimating stochastic reaction constants from molecule count data measured, with error, at discrete time points is considered. For modelling the system, a hidden Markov process is used, where the hidden states are the true molecule counts, and the transitions between those states correspond to reaction events following collisions of molecules. Two different algorithms are proposed for estimating the unknown model parameters. The first is an approximate maximum likelihood method that gives good estimates of the reaction parameters in systems with few possible reactions in each sampling interval. The second algorithm, treating the data as exact measurements, approximates the number of reactions in each sampling interval by solving a simple linear equation. Maximising the likelihood based on these approximations can provide good results, even in complex reaction systems.

Algorithms↗

PubMed2003

Properties of perimetric threshold estimates from full threshold, ZEST, and SITA-like strategies, as determined by computer simulation.

PURPOSE: To investigate the accuracy and precision of threshold estimates returned by two Bayesian perimetric strategies, staircase-QUEST or SQ (a Swedish interactive threshold algorithm [SITA]-like strategy) and ZEST (zippy estimation by sequential testing), and to compare these measures with those of the full-threshold (FT) algorithm. METHODS: A computerized visual field simulation model was developed to compare the performance (accuracy, precision, and number of presentations) of the three algorithms. SQ implemented aspects of the SITA algorithm that are in the public domain. The simulation was tested by using standard automated perimetry (SAP) visual field data from 265 normal subjects and 163 observers with glaucomatous visual field loss and by exploring the effect of response variability and response errors on algorithm performance. RESULTS: SQ was faster than FT or ZEST, with a comparable mean error when simulating field tests on patients. Point-wise analysis revealed similar error and standard deviation of error as a function of threshold for FT and SQ. If the initial estimate of threshold for either procedure was incorrect, the means and standard deviations of the error increased markedly. ZEST produced more accurate thresholds than did the other two strategies when the initial estimate was removed from the true threshold. CONCLUSIONS: When simulated patients made errors, the accuracy and precision of sensitivity estimates were poor when the initial estimate of threshold either overestimated or underestimated the true threshold. This was particularly so for FT and SQ. ZEST demonstrated more consistent error properties than the other two measures.

Algorithms↗